Software Updates and Releases for Electron Microscopy Instruments

SPA acquisition software

Description of updates

• Smart EPU is enabled by the new CryoFlow software, which serves as a successor to Athena software.
• Embedded CryoSPARC Live multigrid support:
  During a Multigrid session with a prepared single session using an Embedded CryoSPARC Live dataset, when the user:
  • Clicks on the Auto-create sessions button in the Session Queue task to create sessions for all slots.
  • Clicks on the Add Session button in the Session Queue task to create a single session.

  Then the new session(s) have a dataset automatically created with the same parameters as the prepared single session.

  • Min & Max Particle Diameter
  • Extraction Box Size
  • Particle Downsampling (Desired Approx. Pixel Size)
  • Picking Shape
• Plasmon peak imaging works with embedded Gatan BioQuantum/BioContinuum filters.

Watch this tutorial to learn how to use new features in this release.

Note: Legacy EPU Software users having a valid EPU license can upgrade to EPU 3.x. If you have Smart EPU Software, please contact service for a combined EPU and Athena software update. Updating only EPU Software can cause an unexpected behavior.

Download release notes for Smart EPU Software 3.9   

Compatibility: Titan SW 3.16.x – 3.21.x / Talos SW: 2.16.x – 2.21.x

For questions, please contact EPU@Thermofisher.com

SPA acquisition software

Description of updates

• Smart EPU with Embedded CryoSPARC Live available for Tundra Systems:
  Tundra systems are enabled to be configured with Embedded CryoSPARC Live for Ceta-F and Falcon C cameras.
  
  
• Plasmon Peak Imaging:
  Plasmon peak imaging is introduced to enhance low ice thickness contrast. This is particularly useful for selecting foil holes in gold grids, where the contrast difference between gold film and ice is large, and the contrast generated by varying ice thickness is low.
  
  
• Smart Ice Thickness Prediction:
  An AI-driven tool for selection of foil holes based on ice thickness ranges assignments. A set of predefined ranges for ice thickness is provided to the user. The tool is primarily designed to be used during sample screening.
  For screening of multiple grids, users can define the conditions for foil hole selection in one grid and apply those to other grids in a queue without exchanging grids.
  
  
• Support for Tilted Acquisition:
  Support for Tilted Grids Acquisition helps the users to cope with samples with preferred orientation in EPU. User will be able to set up and execute runs on grids with a tilt up to 40 degrees. 
  • User can now define an EPU session as a tilt grid session in EPU session setup.
  • User can now set stage tilt in degrees from EPU Area Selection and Hole Selection tasks when they selected tilted acquisition in session setup.
  • EPU now shows the hole indicators as ellipses in the Hole selection and Data acquisition tasks when using tilted acquisition. Shape of the goggles used for hole size and distance measurement in EPU hole selection task has been adjusted for tilted acquisition.
  • User can define the yellow foil hole indicator drawn as an appropriate ellipse in the template definition task and the template execution task at the specified tilt angles.
  • Ice filtering has also been adjusted for tilted acquisition sessions.

Watch this tutorial to learn how recently released features can facilitate sample screening.

Note: Legacy EPU Software users having a valid EPU license can upgrade to EPU 3.x. If you have Smart EPU Software, please contact service for a combined EPU and Athena software update. Updating only EPU Software can cause an unexpected behavior.

Release notes
 

Compatibility: Titan SW 3.15.x – 3.20.x / Talos SW: 2.15.x – 2.20.x. 

For questions, please contact EPU@Thermofisher.com

SPA acquisition software

Description of updates

• New smart selection of grid square plugin automatically selects and categorizes grid squares
  
  The AI-based Smart Selection functionality in the Square Selection task has been extended with a feature allowing you to choose the desired total number of automatically selected grid squares for screening. The selected squares are distributed across categories representing varying ice conditions. For more fine-grained control, users can change the number of squares per category.
  
  This feature is intended to automate the step of grid square selection for screening while retaining control over the selection for advanced users.
  
  
• Manual deselection of grid squares
  
  Users can mark a grid squares as ‘unusable’ in the EPU square selection or hole selection / area selection task, improving the efficiency of manual screening for high-resolution data collections and enable easy transition from screening to high-resolution data collections on demanding samples.
  
  This feature is intended to automate the step of grid square selection for screening while retaining control over the selection for advanced users.

Watch this tutorial to learn how recently released features can facilitate sample screening.

Note: Legacy EPU Software users with a valid EPU license can upgrade to EPU 3.x. If you have Smart EPU Software, please contact service for a combined EPU and Athena Software update. Updating only EPU Software can cause an unexpected behavior.

Release notes

Compatibility: Titan SW 3.14.x – 3.19.x / Talos SW: 2.14.x – 2.19.x. 

For questions, please contact EPU@Thermofisher.com

SPA acquisition software

Description of updates

• Automatic placement of the autofocus area—EPU Software can automatically place the autofocus area at a suitable position for sample carriers with a foil hole pattern with square or hexagonal geometry. During data collections with session type "automated", the autofocus area will be placed on-the-fly. This removes the need to reload each grid of a multigrid queue to generate the optimal template. During data collection with session type "manual", the autofocus area will be placed when the user performs "template definition" task. Users could adjust the position manually, which automatically deactivates the feature.
• Smart Filter for Grid Squares (Beta)—An AI-based filter to automatically deselect the grid squares that are not appropriate for data collection is available in the "Square Selection" task in the "EPU" tab. This feature flattens the learning curve for novice users and further streamlines the data collection setup.
  Requires “Smart EPU with EQM” or “Smart EPU with Embedded CryoSPARC” license.
• Falcon C Detector support—A new direct electron detector, optimized for 100 kV (Tundra Cryo-TEM) is released and available in EPU Software. Users can perform image acquisitions using either counting (best image quality, preferred for high-resolution reconstructions) or linear (shortest acquisition times, preferred for sample screening) mode. Advised preferences for the Falcon C camera are available on the EPU Software landing page.
• Grouping by Image Beam shift—Data generated during automated data collection using Acquisition mode “Faster” (AFIS) now contain information about the image beam shift group in the filename (FoilHole_20007835_Data_20008808_nnn_20210420_154730), enabling easy state-of-the-art aberration correction.
• Creating Athena Software folders and workflows—It is possible to create Athena Software folders and workflows in EPU Software.

Watch this tutorial to learn how recently released features can facilitate sample screening.

Note: Legacy EPU Software users with a valid EPU license can upgrade to EPU 3.x. If you have Smart EPU Software, please contact service for a combined EPU and Athena Software update. Updating only EPU Software can cause an unexpected behavior.

Release notes

Compatibility: Titan SW 3.13.x – 3.18.x / Talos SW: 2.13.x – 2.18.x.

For questions, please contact EPU@Thermofisher.com

SPA acquisition software

Description of updates

• Compression for Data Acquisition Images:
  • On systems with the Falcon 4i Detector, you can enable LZW Compression for Data Acquisition images at Preparation > Exposure Settings > Compression. The compression is applied on Data Acquisition images stored in TIFF at native 4k x 4k resolution.
  • This feature uses non-gain-normalized compression.
  • To activate this feature, set Fractions to manual or max, specify the number of fractions desired, and set Compression to Yes.
  • Note: Requires TEM Server 7.17 (Titan 3.17 / Talos 2.17).
• Gain Reference Copy for EER or TIFF Output: When using a Falcon 4i Detector and EER or TIFF as output for the data acquisition preset, a copy of the gain reference is now supplied in the folder containing the movies.
• Guided Image Shift Calibration: The previous UI for this calibration has been completely redesigned to make it easier and more efficient to use. We've introduced a visual guide that walks you through the calibration process step by step. This guide simplifies the process and reduces the need for extensive user experience. Additionally, it includes the option to perform Auto Eucentric during calibration, ensuring valid results and saving you time.
• Stored Image Shift Calibration for New Sessions: EPU now saves the results of your image shift calibrations, allowing you to reuse them in new sessions. This reduces the time needed for recalibration and ensures that the settings are appropriate for each specific session. Here's how it works:
  • When creating a session from advised preferences, any saved calibrations associated with these preferences will be automatically applied.
  • If you're creating a session from a favorite preference and no calibration data is available, the calibration will start from the default position.
  • After a successful calibration, the new calibration data is saved and can be reused in future sessions. This is especially beneficial when using favorite preferences because the saved calibration data is automatically updated.
• Enhancements to User Alignments: Among several efficiency and user-friendliness enhancements, we highlight the following:
  • Improved Pop-up Dialogue for User Alignments: The pop-up dialogue for User Alignments on Tundra Cryo-TEM systems has been improved to display the alignments to be performed, the estimated time of the sequence, and a Stop button for long alignments. It also provides success and failure indicators for the recovery procedure.
  • Automatic Closure of Column Valves: After user alignments are recovered using the recovery button, column valves will now close automatically, saving you an extra step.
• Enhanced Traffic Light: The Traffic Light now displays a third state, blue, in addition to the existing red and green states. The blue state indicates a medium severity issue. This enhancement provides a clearer understanding of the system state.
  • Note: Requires TEM Server 7.17 (Titan 3.17 / Talos 2.17)
• MiCo Link on EPU Landing Page: A button with the Microscope Companion (MiCo) logo has been added to the EPU Landing Page. This button is enabled when MiCo is installed on the microscope PC and is available for entry level and midrange systems.

Watch this tutorial to learn how recently released features can facilitate sample screening.

Note: Legacy EPU Software users with a valid EPU license can upgrade to EPU 3.x. If you have Smart EPU Software, please contact service for a combined EPU and Athena Software update. Updating only EPU Software can cause an unexpected behavior.

Compatibility: Titan Cryo-TEM SW 3.12.x – 3.17.x / Talos TEM SW: 2.12.x – 2.17.x. 

For questions, please contact EPU@Thermofisher.com

SPA acquisition software

Description of updates

• We introduce Open API, allowing you to develop custom plugins that interact with Smart EPU Software utilizing AI/ML capabilities for evaluating microscope output and adjusting settings while fostering collaboration within the cryo-EM community.
• The Center C2 aperture block in SA Microprobe (uP) mode on Tundra Cryo-TEM systems now centers the 150μm C2 aperture as well. For more details, refer to the MiCo (Microscope Companion) manual.
• The Optimize Beam function has been renamed to Optimize Optics and can now be found in the Autofunctions tab.
• Alignments has been renamed to User Alignments and is now accessible in the Traffic Lights section on Tundra Cryo-TEM systems. On Glacios Cryo-TEM systems, the User Alignments can be accessed via MiCo.
• The Objective Aperture is no longer retracted after executing the Optimize Optics (formerly Optimize Beam) sequence.
• Traffic Lights have been updated to display more informative messages for warning states (blue) and error states (red).
• The Ice Filter feature on CFEG systems now compensates for beam-current fluctuations, providing consistent hole selection during EPU multigrid runs.
• Template Definition task > Defocus List now uses the Defocus List of the previous acquisition area by default.
• The Smart Filter button is now a toggle button, with its function being applied after holes are found.
• The Hole Selection task > Fast Screening feature has been moved from the expandable panel of the Selection ribbon group to the main ribbon, to increase its visibility. The slider is replaced by a text field, and the maximum limit for the number of locations is increased from 10 to 50.

Watch this tutorial to learn how recently released features can facilitate sample screening.

Note: You can upgrade to EPU Software 3.x if you have a valid EPU license. If you have Smart EPU Software, please contact service for a combined EPU and Athena Software update. Updating only EPU Software might break compatibility with processing and smart automation features.

SPA acquisition software

Description of updates

• Smart EPU
  • A new Athena Software add-on, the Discovery Viewer, allows you to investigate the exact grid square and foil hole where an image was acquired. This feature requires you to create a new Athena workflow under EPU 3.3 and Athena 1.19. Workflows (and datasets within workflows) created under earlier versions are not supported.
  • Smart Filter supports Hexagonal grids under the Holey Gold type.

• EPU
  • Advised preferences are now provided for Glacios Cryo-TEM
  • Auto Functions tab: For each Auto Function task, EPU Software now selects the relevant preset automatically. For example, the Focus preset is automatically selected for the Autofocus task.
  • Acquisition and Optics Settings task: The ribbon is now much cleaner. Some parameters have been removed; others moved to the ribbon's expandable menu.
  • Optics settings of high SA presets can be linked to the Data Acquisition preset.
  • When an incompatible version of Athena Software is used with EPU Software, a warning message shows on startup.
  • The default path for data storage is drive D (if available).
  • The file naming convention for Atlas data gives each Atlas a unique name.
  • The Objective Aperture is now left inserted after the Optimize Beam (Optimize Optics) sequence.
  • On Tundra systems: The Center C2 aperture block in SA uP mode now also centers 150 µm apertures. For more details, please refer to the MiCo User Manual.

Watch this tutorial to learn how to use Discovery Viewer to identify grid areas for high-quality data acquisition.

Note: You can upgrade to EPU 3.x if you have a valid EPU license. If you have Smart EPU please contact service for a combined EPU and Athena software update. Updating only EPU might brake compatibility with processing and smart automation features.

Compatibility: Titan SW 3.10.x – 3.15.x / Talos SW: 2.10.x – 2.15.x. 

For questions, please contact EPU@Thermofisher.com

SPA acquisition software

Description of updates

• Smart EPU with EPU Quality Monitor or with Embedded CryoSPARC Live
  • EPU supports integration with Embedded CryoSPARC Live.
  • An improved version of the Smart Filter functionality is available. Smart Filter automatically filters out obviously bad foil holes in a Gridsquare.
  • Smart Filter now works with Holey Gold grids.
  • Smart Filter works better with other filters such as the Remove Grid Holes Close to Grid Bar filter and the Ice Filter.
• EPU Multigrid
  • Rather than manually creating individual sessions in the Multigrid queue, you can now use the Auto-create Sessions functionality to automatically create identical sessions--one for each acquired Atlas--and add it to the Multigrid queue.
  • Sessions with incomplete parameters are now clearly indicated.
  • Upon automatically adding sessions to the MultiGrid queue, a pop-up informs you of those located on the C-drive.
  • In the Multgrid queue, the Atlas of the selected session is shown at the bottom of the session's info.
  • You can now create a Multigrid queue right from the Home tab.
• General Improvements
  • The two buttons Create session from preferences and Save session to preference have been removed from the EPU tab. In order to import your EpuSessionPreferences files, use the Home > Saved Preferences > Import button. This will place your imported session in Saved Preferences. You can then create a session from Saved Preferences at any time.
  • Improved instructions for running Optimize Beam.
  • The image quality during preparation is now as high as a preview or an image acquired during an automated run.

To obtain update:

Note: You can upgrade to EPU 3.x if you have a valid EPU license. Some of the Smart EPU features will need a full upgrade of Athena performed by service and depend on the existence of certain additional packages.

SPA acquisition software

Description of updates

• Smart EPU with EPU Quality Monitor or with Embedded CryoSPARC Live
  • EPU now has a dedicated grid type for Holey Gold grids. This grid type also supports hexagonal layouts of foil holes. This feature is in Beta release.
  • Smart Filter is a new functionality that automatically filters out and de-selects inappropriate holes during Hole Selection. The button is found in the Selection ribbon group. Smart Filter works with Prepare All Squares. It is executed for each gridsquare during the execution of an automatic recipe. This feature is in Beta release.
  • Certain features (EQM, Smart plugins) are disabled when unusable or irrelevant to the selected settings.
• EPU Multigrid
  • In the MultiGrid queue, it is now possible to delete individual EPU sessions.
• General Improvements
  • To save storage space with EPU fractions files, the Compression option is available in the Data Acquisition Preset when supported. Requires Falcon 4(i) camera and TEM 7.13 and higher.
  • Trial License: EPU now allows users a trial period valid for three months after which one can buy a license in order to continue using EPU.
  • In EPU Template Definition and Area Selection, the visualized beam diameter now better represents the actual beam diameter on the system.

To obtain update:
 

Note: You can upgrade to EPU 3.x if you have a valid EPU license. Some of the Smart EPU features will need a full upgrade of Athena performed by service and depend on the existence of certain additional packages.

SPA acquisition software

Description of updates

• The Home Page is available on all configurations, it allows easy management of favorite settings and contains various useful shortcuts.
• A Fast Screening option is added, which automatically selects a few holes per gridsquare to easily screen grids. This feature can also be used in combination with Multigrid to efficiently screen many grids.
• In Hole Selection the ribbon has been cleaned up, several options are now available through a flapout.
• Targeting accuracy has been improved, leading to better positioned micrographs during Automated Acquisition.
• The Atlas Alignment procedure has been improved to be more robust and accurate when loading a grid on the stage or when executing a Multigrid session.
• More guidance has been added to Multigrid.
• Various ice filter improvements have been added, including context menu shortcuts for easier adjustments.
• The Pause button in Automated Acquisition has been removed.
• The application startup has been improved.
• Several other small improvements and fixes.

Release notes

SPA acquisition software

Description of updates

• EPU Software automatically opens the column valves when needed.
• In combination with TEM Server 7.11 (Titan 3.11 / Talos 2.11) several image acquisitions functionalities have been optimized to further increase throughput for the Thermo Scientific Falcon 4i Detector.
• The “Session Setup” tasks have been revised and simplified.
• The calibration of AFIS clusters has been improved by measuring the actual attainable image beam shift range.
• Lens normalizations have beam improved to reduce navigation inaccuracies.
• The Auto Zero-Loss auto-function for Gatan BioQuantum and BioContinuum filters is more robust.
• An issue with the objective aperture during screening has been resolved.

Release notes

SPA acquisition software

Description of updates

• AFIS/clustering range increased to 12 μm resulting in less stage moves and increased throughput for "Fast Acquisition" mode.
• In combination with TEM Server 7.10 (Titan 3.10 / Talos 2.10) several image acquisitions functionalities have been optimized to further increase throughput.
• When available EPU uses and reports the dose that is calculated by the camera that is compensated for coincidence loss, the dose measurement is more accurate than previously calculated by EPU.
• Improvements in screening workflow.
• For “auto-eucentric by stage tilt” the "minimum cross correlation quality" parameter is replaced by the more user-friendly "maximum z-height deviation".

Release notes

SPA acquisition software

Description of updates

• Screening functionality is now enabled also on side-entry loader systems
• Gatan K3 camera dark reference acquisition is now configurable
• The accuracy of automated acquisition in automatically re-loaded samples (e.g., multigrid) is improved
• Various other performance improvements and bug fixes
• Resolved issue for 2.12 Win 7

Release notes

SPA acquisition software

Description of updates

• Manually add grid-squares on custom positions.
• A traffic light for system readiness and recovery is now available on all Krios configurations, model G3 or later. Requires Titan 3.8 or later.
• A new, more efficient way to calculate stage settling time after moving.
• Time-based Gatan K3 Dark Reference image acquisition.
• Multiple smaller fixes and performance improvements.

Release notes

SPA acquisition software

Description of updates

• A traffic light reports the system readiness status for a successful high-quality data acquisition. If this traffic light is not green for all monitored parameters, then the Recover function automatically adjusts the parameters that are out-of-range. The traffic light and recovery functions are only available on Krios systems with TEM Server 7.7 or later, and a Falcon 4 camera in bottom-mounted or post-filter position.
• The EPU Multigrid option enables the consecutive execution of multiple Automated Acquisition runs.

Release notes

*Multigrid availability:

• Free for (Titan) Krios systems with Windows 10 (upgrade)
  
• Paid option for all other systems

SPA acquisition software

Description of updates

• EPU > Hole Selection and Area Selection, and EPU > Automated Acquisition: In manual mode, the Alpha tilt angle at which each individual Grid Square is prepared is automatically applied again during the Automated Acquisition run.
• EPU > Automated Acquisition: The MRC2014 FEI2 Extended Header image format is introduced. Among other specification improvements, the FEI2 Extended Header specification contains more metadata fields than the FEI1 Extended Header. The FEI1 Extended Header format is now frozen, it will no longer be extended with new metadata. Some of the new metadata fields in the FEI Extended Header are not filled yet.
• EPU > Automated Acquisition: The throughput for the Gatan K2 camera is improved. Requires TEM Server 7.6 or later

Release notes

SPA acquisition software

Applicable instruments

• Krios G3
• Krios G3i Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
  
• Talos F200C
• Talos L120C

Description of updates

• Atlas > Screening: Automated Atlas Alignment after Load Sample
• EPU > Session Setup: The New Session function offers an option to create the new EPU Session with the same settings and parameter values as the current EPU Session
• Hole Selection and Area Selection: The new Automated Preparation functions significantly decrease the amount of time and effort that is needed to manually select the acquisition targets for EPU session
• Automated Acquisition: On systems with a CFEG, the tip is automatically flashed during the Automated Acquisition run to ensure a stable and optimal `electron beam. (requires Titan R3.5.x or later).

Release notes

SPA acquisition software

Applicable instruments

• Krios G3
• Krios G3i Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
  
• Talos F200C
• Talos L120C

Description of updates

• Improvements in square selection and hole selection for a smoother workflow:
  • No longer need to move with the stage to navigate through grid-square images for hole selection.
  • Option to navigate between grid-square images directly from the hole selection page.
  • Various other usability enhancements.
• Automatic periodic acquisition of dark reference images for Gatan K3 camera (requires server version 2.4 (Talos)/3.4 (Krios) or later).
• Improvements in square selection and hole finding algorithms, especially for gold grid specimens.
• Improvements in targeting accuracy and throughput of “Fast acquisition”.
• Various usability and performance improvements as well as bug fixes, including:
  • Ability to copy template defocus list to all areas with one click.
  • Warning for the AutoLoader TMP running when starting a new Automated Acquisition.
  • Simplified look and feel for Atlas Screening.

Release notes

SPA acquisition software

Applicable instruments

• Krios G3
• Krios G3i Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
  
• Talos F200C
• Talos L120C
  

Description of updates

• Acquisition and Optics Presets: The Falcon 4 camera is now available
• Fast acquisition mode:
  • Targeting accuracy is improved. For every Grid Square a foil hole position refinement action improves the hole finding accuracy and a foil hole position correction calibration minimizes the effects of any misalignment
• Smart Grid Square selection:
  • Selection now starts from the categories chosen at screening
  • An algorithm analyzes the user selection and proposes similar grid squares as well as the ability to extend the current selection with the best match from the remaining squares
• Screening:
  • Various improvements including the ability to re-acquire an Atlas and to choose the number of tiles
• Usability improvements:
  • UI responsiveness when changing camera settings is much better
  • Grid Square detection algorithm is significantly improved

Release notes

SPA acquisition software

Applicable instruments

• Krios G3i Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
  
• Talos F200C
• Talos L120C
  

Description of updates

• Gatan BioQuantum 1967 with K3 camera is now also supported in EPU on systems with Titan 3.2.X or later, or Talos 2.2.X software or later.
• Preparations > Acquisition and Optics Presets: The most recent acquired preview for each Present remains available until a new Preview is acquired. On the preview image, the context menu provides navigation options.
• Preparations > Acquisition and Optics Presets: In the Data Acquisition Preset it is possible to select the C2 Aperture. The other Presets automatically use the same C2 Aperture, except for the Atlas Preset, which will always use the largest available C2 Aperture.
• Atlas > Screening: In the Data Acquisition Preset it is possible to select the C2 Aperture. The other Presets automatically use the same C2 Aperture, except for the Atlas Preset, which will always use the largest available C2 Aperture.
• Atlas > Acquire Atlas: The Load from Screening function imports the Atlas for the loaded specimen from the Screening task. This way, no new Atlas needs to be acquired. If the specimen has rotated or has otherwise shifted, then it is still possible to acquire a new Atlas.
  
  
• Improvements and other changes:
  • EPU > Template Definition: The Defocus List is simplified, so it is much more user-friendly to create, edit and remove defocus values, and to copy defocus lists to existing Acquisition Areas.
  • EPU > Template Definition: The position of an Acquisition Area relative to the center of a Foil Hole is no longer specified in separate X and Y distances, but as the radial distance.
  • EPU > Setup Session: The selection of values and settings that is supported by the Session Preferences is extended with Hole Selection, Area Selection and Automated Acquisition Settings (incl. Phase Plate settings).
  • EPU > Hole Selection and EPU > Automated Acquisition: The accuracy of the Find Holes function is significantly improved.

Release notes

SPA acquisition software

Applicable instruments

• Krios G4 Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
  
• Talos F200C
• Talos L120C

Description of updates

• Up to double throughput by using “Faster Acquisition” mode that utilizes Aberration Free Image Shift (AFIS requires at least Titan 2.15) in combination with hole clustering
• Lacey carbon by default uses Faster Acquisition mode if available
• Option for fast session setup from previously saved preferences that include Camera and Optics settings, session information and template definition
• Support for the Gatan Bioquantum K3 detector (requires Titan 2.15.2):
  • Asynchronous data acquisition for maximum throughput
  • Support for LZW compressed TIFF output format for dose fractions
• Usability improvements:
  • Objective aperture automatically retracted for Atlas acquisitions
  • Ability to load cartridge to stage from within the EPU Screening task
• Various performance improvements and bug fixes

Availability

• Included in service contracts
• EPU 2.x is only available on Titan 2.12 and later, and Talos 1.12 and later
• EPU 2.x does not support the Falcon 2 camera
• EPU 1.x can be updated to EPU 2.x in case of service contract, it does not require license renewals.

Release notes

Electron Diffraction acquisition software

Description of updates

• Compatibility with new Titan and Talos software versions. No major updates.

Download release notes for EPU-D Software 1.20.

Electron Diffraction acquisition software

Description of updates

• Compatibility with new Titan and Talos software versions. No major updates.

Release notes

Electron Diffraction acquisition software

Description of updates

• Compatibility with new Titan and Talos software versions. No major updates.

Release notes

Electron Diffraction acquisition software

Description of updates

• Compatibility release. No major updates.

Release notes

Electron Diffraction acquisition software

Description of updates

• Compatibility release. No major updates

Electron Diffraction acquisition software

Description of updates

The EPU-D 1.15 release does not introduce new features or major improvements. It maintains compatibility with new Titan and Talos TEM software versions.

Electron diffraction acquisition software

Description of updates

• Acquisition and Optics Settings task: The ribbon is now much cleaner.
• Some parameters have been removed; others moved to the ribbon's expandable menu. The default path for data storage is drive D (if available).

Electron Diffraction acquisition software

Description of updates

• Bug fixes and TEM server compatibility
• Improvements in optics handling are introduced to avoid center stop drifting away from beam stop position
• Optimized position is now also used during batch acquisition

Electron Diffraction acquisition software

Applicable instruments

• (Titan) Krios
• Glacios
• Talos Arctica

Description of updates

• General: Improvements in optics handling are introduced to avoid center stop drifting away from the beam stop position.
• Acquisition: Optimized position calibration is now also used during batch acquisition.

Release notes

Electron Diffraction acquisition software

Applicable instruments

• (Titan) Krios
• Glacios
• Talos Arctica

Description of updates

• TEM Server compatibility release

Release notes

Electron Diffraction acquisition software

Description of updates

• Acquisition: The MRC2014 FEI2 Extended Header image format is introduced. Not all new metadata fields are filled yet.

Release notes

Electron Diffraction acquisition software

Applicable instruments

• Glacios Cryo-TEM
• Talos Arctica TEM

Description of updates

• Session Setup:
  • Tilt Series can now be stored as SMV files.
• Automated Acquisition:
  • The Image Display can now show the Tilt Axis.
  • The Image Display can now toggle between Diffraction and TEM Imaging mode.
  • An acquired Tilt Series can now be played back as a video.
  • An acquired Tilt Series can now be exported as an H.264 MPEG4 video.

Micro Electron Diffraction (MED / Micro-ED) acquisition software

Applicable instruments

• Glacios Cryo-TEM
• Talos Arctica TEM
  

Description of updates

• Beta Batch feature that includes:
  • Definition of multiple positions to be acquired in a sequence.
  • Ability to pre-visit all defined positions to acquire a diffraction screening image.
  • Acquisition of reference imaging mode picture before screening/tilt series.
  • Visualization of the results.
• The Atlas screening task for systems with AutoLoader is now available in EPU-D as well.
• Ability to inspect the intensity and resolution of a specific point in diffraction patters.
• Various usability and performance improvements including:
  • Control of the C2 aperture via the presets.
  • Improved auto-contrast brightness behavior during tilt series acquisition.

Release notes

Micro Electron Diffraction (MED / Micro-ED) acquisition software

Applicable instruments

• Glacios Cryo-TEM
• Talos Arctica TEM

Description of updates

• Licensing: a 30-day Trial License is available
• Optimized Position calibration to compensate for an offset between the tilt axis of the stage and the optical center of the aligned column
• Session Setup: acquired images can be saved as a single stacked MRC image file per Tilt Series

Release notes

Micro Electron Diffraction (MED / Micro-ED) acquisition software

Applicable instruments

• Glacios Cryo-TEM
• Talos Arctica TEM

Description of updates

• Image Display:
  • Resolution Rings: this Image Display overlay gives a quick overview of the resolution of the diffraction pattern. This overlay can easily be centered with the diffraction pattern.
  • Diffraction Ruler: this Image Display overlay enables an easy method to measure the resolution of a particular bright spot.
  • Frame Slider: after the acquisition of a Tilt Series is completed, the Frame Slider enables inspection of the acquired images.
• Atlas: An automatic check validates the integrity of a loaded Atlas.
• Automated Acquisition:
  • Name: each Tilt Series must have a unique name. This name is included of the file-path for the acquired images.
  • Auto Eucentric: automatically sets the specimen to eucentric height, using the stage tilt method.
  • Histogram > Reset Auto Levels: reverts custom contract, brightness and gamma to the values that are calculated by the auto-level algorithm.
• Improvements:
  • Automated Acquisition: The automatic contrast-brightness is improved.

Release notes

Micro Electron Diffraction (MED / Micro-ED) acquisition software

Applicable instruments

• Glacios Cryo-TEM
• Talos Arctica

Description of updates

• This is the first release of the EPU-D software. The EPU-D software is a new product in the range of Thermo Scientific TEM Cryo-EM application software products

Availability

• Included in Micro ED commercial package

Release notes

Image acquisition and processing software (for TOMO) to obtain the complete visual content of a sample

Description of updates

• TEM: Added support for TEM 3.20 and TEM 2.20
  Maps 3.29.1 supports TEM server versions 3.15–3.20 for Titan and 2.15–2.20 for Talos.

   

Description of updates

• TEM: Added support for TEM 3.19 and TEM 2.19
  Maps 3.28.1 supports TEM server versions 3.14–3.19 for Titan and 2.14–2.19 for Talos.

   

• TEM: Standalone Velox plugin
  Acquisition of EDS tile sets through Velox is now available as a standalone plugin, so connectivity to Velox and the acquisition process is more robust.
  
  
• TEM: Tiling correction
  You can use the Tiling Correction beta feature to achieve better tile alignment during acquisition.

Image acquisition and processing software to obtain the complete visual context of a sample

Description of updates

• TEM: Added support for TEM 3.18 and TEM 2.18:

  Maps now supports the latest TEM server versions for Titan (TEM 3.18) and Talos (TEM 2.18).

• TEM: Backlash compensation enhancement:

  Tile set acquisition was enhanced to avoid unnecessary backlash compensation between autofocus and acquisition, while keeping the overall precision of movement during acquisition. Previously, backlash compensation had undesirable consequences when it was applied after autofocus was measured on a first or selected tile, thus leading to out-of-focus results.

• TEM: EDS tile sets saved as template:

  You can now save EDS tile sets as templates and use them when creating or stamping new tile sets. Users no longer have to manually re-select EDS acquisition for these new tile sets. All new EDS tile sets retrieve current EDS acquisition parameters from the Velox application automatically when they are created or copied.

• TEM: Temporary EDS data deletion:

  Maps now automatically deletes temporary files that are saved on the system during EDS acquisition. Previously, users had to manually delete the temporary files. Note that all important files, including EDS maps and metadata, are retained in the Maps project folder.

Image acquisition and processing software to obtain the complete visual context of a sample

Description of updates

• TEM—OptiSTEM autofunction automatically restores last known good state.

  When the OptiSTEM autofunction fails to converge, or when the quality of the result is poor, the Maps Software application automatically restores the focus and stigmator values to the last known good state.

• TEM—Added support for TEM 3.17 and TEM 2.17

  Maps Software now supports the latest TEM server versions for Titan (TEM 3.17) and Talos (TEM 2.17) TEMs.

Image acquisition and processing software to obtain the complete visual context of a sample

Description of updates

• Animation for viewer functions:
  The “Center View on Sample,” “Center View on Selection,” and “Go to Microscope FOV” viewer functions in the toolbar now animate pan and zoom to help keep you oriented in the sample space. If desired, you can deactivate this feature under the “Animate Pan & Zoom” View menu item.
  
  
• EFTEM slit control:
  Slit insertion state and energy-selecting slit width can now be set directly on a tile set. Slit parameters are also now part of EFTEM tile set templates and are propagated from Tomography Software presets when importing the presets to Maps Software.
  
  
• Project History search bar: 
  The Project History window now has a search bar available. When you use this search bar, it immediately filters the project history and provides results that match either the Project Name or Project Description fields.
  
  
• TEM/EFTEM: Automated image filtering for autofunctions
  TEM and EFTEM autofunctions support a new setting called "Use Image Filtering". You can use this new setting to improve the reliability and accuracy of these autofunctions.
  
  
• TEM: Added support for TEM 3.16 and TEM 2.16
  Maps Software now supports the latest TEM server versions for the Titan Cryo-TEM (TEM 3.16) and Talos TEM (TEM 2.16).

Image acquisition and processing software to obtain the complete visual context of a sample

Description of updates

• TEM: Added support for TEM 3.15 and TEM 2.15
  Maps Software now supports the latest TEM server versions for Titan TEM 3.15 and Talos TEM 2.15.
  
  
• TEM: Data Exchange with Tomography
  The integration between Maps Software and Tomography Software has been enhanced to support cryo-ET scenarios. The following data can now be automatically synchronized between both applications:
  • Annotations created in Maps Software, including sites of interest, areas of interest, and lamella information
  • Batch positions created in Tomography Software, including exposure, tracking, focus, and condition areas

• TEM: OptiSTEM autofunction (beta)
  The OptiSTEM autofunction has been added to the list of supported autofunctions on STEM as a beta feature. This autofunction corrects defocus and condenser astigmatism (A1/C1). It requires Thermo Scientific Sherpa Software with the OptiSTEM license to be installed on the system. This feature is only available on 2.15 and 3.15 TEM Server versions.
  
  
• TEM: Temporary data default location
  Previously, temporary data created by Maps Software on TEM was stored on the system drive (C:). The default location has been changed to the data drive (D:) to provide more effective management of free space and backups on the system drive. The data written to D: drive includes EDS maps from Velox Software and intermediate images produced during acquisition (that is, when image logging is activated).

Image acquisition and processing software to obtain the complete visual context of a sample

Description of updates

• Move or rotate multiple tile sets
• Tile sets and other movable objects can now be moved or rotated together when using mouse drag and multiselect.
• Stitch option is now compatible with multi-select
• Multi-select can be used to queue multiple tile sets when initiating stitching.
• SDB/SEM microscope settings
• A new setting for the electron beam, "Beam wake up time," has been added.
• A new alignment, "Magnification correction (Electron)," has been added.
• The "Stage alignment (Electron)" setting has been renamed to "Scan rotation correction (Electron)".
• End user license agreement moved to application launch

Maps Software no longer presents the end user license agreement during the application installation process. Instead, it now prompts you to read the end user license agreement immediately after you launch the application.

Image acquisition and processing software (for TOMO) to obtain the complete visual content of a sample

Applicable instruments

• Krios G4 Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
  
• Talos L120C

Description of updates

• Amira-Avizo2D support

TEM User Interface to set up data acquisition

Description of updates

This release includes new features for Autoloader microscopes (Krios, Glacios, and Arctica):

• Temperature and liquid nitrogen display for column and autoloader.
• Temperature mode control (Room temperature and Cryo temperature).
• Cryo Cycle for column and/or autoloader.
• Error reporting of autoloader and/or column filling.

Minor improvements for EDS detector and heating cycle.

Download release notes for MiCo Software 1.14

TEM User Interface to set up data acquisition

Description of updates

• Minor improvements for facilitating automated alignments for applicable microscopes.

Release notes

Description of updates

• Minor improvements for the heating cycle for applicable microscopes.

Release notes

Description of updates

• The heating cycle for applicable microscopes is released in the 1.11 version of the MiCo Software.

Application to prepare TEMs for data acquisition

Description of updates

• Introduction of an Actions page instead of Vacuum and Stage page:
  • The Actions page now contains Cryo-cycle, Recover Stage, Evacuate Column, Recover Optics Boards, Recover Electron Beam
  • The Home page now contains Open/Close column valves and insert/retract stage (for supported stages only).
• Setting of Spotsize and Probe Mode is now added to the header

Application to prepare TEMs for data acquisition

Description of updates

• Recovery of the Optics Board after degradation can now be performed on the Optics page.
• Camera names are presented on the Detector Page.
• Falcon Reference Image Manager is now accessible on the Detector page.
• The measured HT value is now accessible on the Electron Beam page.

TEM user interface to set up data acquisition

Description of updates

• Layout improvements of the detector page
• High Tension value is displayed on Electron beam page
• Removed the layout button on the toolbar
• Disable auto temperature control for UltraX to prevent cooling the detector in case of absence of liquid nitrogen

TEM User Interface to set up data acquisition

Description of updates

• Various updates regarding automated alignments
• More flexibility in the width of the hardware control panels
• Custom manual magnification correction to system calibration
• Smartcam contrast modes (natural, linear high contrast)

To obtain update:

TEM User Interface to set up data acquisition

Description of updates

• Renamed the application from Apollo to Microscope Companion, nicknamed MiCo.
• Updated cryo-cycle on supported systems.
• Stage Recovery.
• Optics page with Beam Diameter control on supported systems.

To obtain update:

Server software for life sciences

Description of updates

High-end TEMs:

• Beam Tilt Pivot Points Alignment
  Beam Tilt Pivot Points work without predefined models.
  
  
• SFEG
  In SFEG systems, there has been a change in the default ramp-up to extraction voltage. The default value has been increased to 4500V, up from the previous value of 3950V. This new default value aligns with the recommended voltage for optimal performance and reduces the risk of a ring collapse.
  
  
• SmartStage
  In Configurator is now possible to select these features:
  • SmartStage Motion Controller – SSC
  • Vacuum System – Titan Basic G2.1
  • High Accuracy Beta Tilt Holder
    

• MyMicroscope Software Agent
  A new version of MyMicroscope Software Agent (MMSA) on TemPrerequisites media to keep the software agent up to date.
          New version “mmsa-1.16.0.1870”
          Old name: “MyMicroscope Software Agent”
          New name: “Thermo Scientific MyMicroscope Software Agent”
  
  
• 90-degree alpha tilt NSR feature
  The 90-degree alpha tilt NSR feature has been relocated from the NSR page to the Motion page in the MasterInstaller Configurator. This feature can now be selected when the CompuStage Mark II option is chosen.
  
  
• HABT
  Added support for the HABT GX Holder type.
  The alpha tilt range of a HABT GX holder is limited to +/-40 degrees. This range is different from other HABT holders, which typically have a range of +/-50 degrees. In the 7.19.1 release, there was a change applied to the HABT GX holder to align its alpha tilt range with the other HABT holders at +/-50 degrees.
  
  
• MPC OS Hardening
  The Windows OS Hardening (Security Policy settings) is included in the "TEM Prerequisites Installer" and is designed to be used with MPC Operating System Image M17 or newer. Starting from TEM version 7.20, the OS Hardening feature will be enabled by default as part of the "TEM Prerequisites Installer."
  
  
• RF Cavitymart
  Direct alignment for a RF Cavity. The features is available in TEM > Imaging > Parallel mode.

Mid-range TEMs:

• Beam Tilt Pivot Points Alignment
  Beam Tilt Pivot Points work without predefined models.
  
  
• Gun lens controls
  In Talos E-CFEG systems, there has been a change in the accessibility of gun lens controls (index, coarse, and fine) of the FEG OCX (PEO UI). Previously, these controls were restricted to the 'service' user and above. With the latest update, these controls are now available to the 'supervisor' user and above.
  The User Alignments sequence now supports Gun Lens 1.
  
  
• SFEG
  In SFEG systems, there has been a change in the default ramp-up to extraction voltage. The default value has been increased to 4500V, up from the previous value of 3950V. This new default value aligns with the recommended voltage for optimal performance and reduces the risk of a ring collapse.
  
  
• Master Installer and Configurator
  FringeFree is one of the selectable options for the Glacios microscope type in the MasterInstallers Configurator, on the Optics page.
  
  
• MyMicroscope Software Agent
  A new version of MyMicroscope Software Agent (MMSA) on TemPrerequisites media to keep the software agent up to date.
          New version “mmsa-1.16.0.1870”
          Old name: “MyMicroscope Software Agent”
          New name: “Thermo Scientific MyMicroscope Software Agent”
  
  
• MPC OS Hardening
  The Windows OS Hardening (Security Policy settings) is included in the "TEM Prerequisites Installer" and is designed to be used with MPC Operating System Image M17 or newer. Starting from TEM version 7.20, the OS Hardening feature will be enabled by default as part of the "TEM Prerequisites Installer."
  
  
• Align Genie
  The Align Genie 1.0 sequence has been enhanced to provide users with the ability to customize the sequence by selecting specific algorithms to be used. Additionally, in the Settings section, users can now choose their desired target magnification range.

Entry level TEMs:

• Beam Tilt Pivot Points Alignment
  Beam Tilt Pivot Points work without predefined models.
  
  
• MyMicroscope Software Agent
  A new version of MyMicroscope Software Agent (MMSA) on TemPrerequisites media to keep the software agent up to date.
          New version “mmsa-1.16.0.1870”
          Old name: “MyMicroscope Software Agent”
          New name: “Thermo Scientific MyMicroscope Software Agent”

• Talos Configurator
  In the Talos Configurator, when entering the Commercial Type number 1508621, the Tundra (EL TEM) option is preselected.
  
  
• MPC OS Hardening
  The Windows OS Hardening (Security Policy settings) is included in the "TEM Prerequisites Installer" and is designed to be used with MPC Operating System Image M17 or newer. Starting from TEM version 7.20, the OS Hardening feature will be enabled by default as part of the "TEM Prerequisites Installer."
  
  
• Cleaning
  Guided cleaning of the surfaces related to the sample transfer for Tundra is introduced and can be found on the left toolbar. It is a multi-step process with detailed instructions.

To obtain update:

Server software for life sciences

Description of updates

High-end TEMs:

• 100 kV Alignment
  The way the vacuum system handles unexpected pressure changes during holder insertion or retraction has been adjusted to enhance the system's robustness against sudden spikes.
  
  
• RF Cavity
  The RF Cavity functionality is now available as a regular commercial option for systems with a CFEG source. RF Cavity is not compatible with the Gun-column integration option.
  
  In the X-CFEG user interface it is possible to enter a more precise Gun Lens index value with up to 3 decimals. This makes it possible to cross the beam more precisely into the RF Cavity module.
  
  
• Vacuum G2.1 (for systems with SmartStage)
  • IGPco > High trip level and PPcl > Medium trip level.
  • IGPco > High trip level for 5 consecutive measurements within 2 seconds.
    This prevents showing a red background in case of a transient pressure spike.

• Falcon 4 and Falcon 4i
  The Falcon 4 and Falcon 4i cameras are now also available on Spectra systems.
  
  
• BSL3
  On systems with the 60º C Heat Decontamination option, the new Heating Cycle Report Generator.
  
  
• Microscope Software Launcher
  The Microscope Software Launcher (MSL) will no longer display a message when virtual memory usage reaches 80%. This is considered normal behavior.
  
  
• SmartStage
  • LoadLock
    The pumping sequences for the LoadLock have been adjusted to enhance the lifetime of the manifold pump (TMPm). The column valves are now closed before any operation involving the LoadLock. 
  • During the Insert and Retract procedures, the T1, T2, and T3 axes will perform a homing procedure to mitigate potential zero-positioning issues.
  • Added support for the HABT GX Holder type.

Mid-range TEMs:

• AAM G2 LS (Long Stroke)
  The Automated Aperture Mechanism (AAM) G2 with Long Stroke option is now available as a standard commercial option on all Talos systems. AAM G2 LS is not compatible with the SCU Based Phase Plate Heating option.
  
  
• Traffic Light: Alignments:
  The Rotation Center on Beam alignment is removed from the User Alignments in EPU and MiCo. This alignment is sufficiently stable and does not require frequent execution.
  The Rotation Center on Image alignment is removed from the User Alignments in EPU and MiCo. This alignment is sufficiently stable and does not require frequent execution.
  The Beam Tilt Pivot Points alignment is removed from the User Alignments in EPU and MiCo. This alignment is sufficiently stable, does not require frequent execution, and affects the AFIS calibration.

Entry level TEMs:

• Traffic Light: Alignments:
  
  
  • The Rotation Center on Beam alignment has been removed from the User Alignments in EPU and MiCo. This alignment is considered stable enough and does not require frequent execution.
  • The Rotation Center on Image alignment has been removed from the User Alignments in EPU and MiCo. This alignmentis considered stable enough and does not require frequent execution.
  • The Beam Tilt Pivot Points alignment has been removed from the User Alignments in EPU and MiCo. This alignment is sufficiently stable, does not require frequent execution, and affects the AFIS calibration.
  
  
• Transfer Device
  
  The connection sequence for the Transfer Device is now more robust against temporary status changes to the Inactive state caused by an unstable Attached sensor.

• Microscope Software Launcher
  
  The Microscope Software Launcher (MSL) will no longer display a message when virtual memory usage reaches 80%. This is considered normal behavior.

To obtain update:

Server software for life sciences

Description of updates

High-end TEMs:

• SmartStage
  
  The way the vacuum system handles unexpected pressure changes during holder insertion or retraction is adjusted, so that the system is more robust against unexpected spikes.

Mid-range TEMs:

• Traffic Light - Alignments
  
  
  • User Alignments
    The speed and robustness are improved. On average, the entire sequence is now completed in less than 20 minutes.
    On Glacios 2 systems with E-CFEG, all User Alignments now use Spot Size 5, and use the currently active Gun Lens.
    
  • The beam detection algorithm for automated EPU and SPA alignments and acquisitions is further improved for maximum robustness and reliability.
  • The beam detection algorithm for Linear Distortion Correction (LDC) on Talos F200E systems is further improved for maximum robustness and reliability.


• Falcon C
  
  The Falcon C camera is now supported by:
  
  • Traffic Light
  • MiCo
  • EPU and eCL
  • EER readerlib decoder (for interfacing with 3rd party software, such as Relion)

Entry level TEMs:

• Alignments and Calibrations
  
  The beam detection algorithm for automated EPU and SPA alignments and acquisitions is further improved for maximum robustness and reliability.
  
  
• Falcon C
  
  The Falcon C camera is now supported by:
  
  • Traffic Light
  • MiCo
  • EPU and eCL
  • EER readerlib decoder (for interfacing with 3rd party software, such as Relion)

• Cryo Loading Station (CLS)
  
  When the LN2 level reaches the Critical level, the LN2 must be refilled within 10 minutes. If LN2 is not refilled within 10 minutes, then an error message appears on the OSD, and a recover action must be executed.

Server software for life sciences

Description of updates

High-end TEMs:

• Alignments and Calibrations
  
  Magnification Calibration (MagCal) now supports the Holography Transfer Lens.

• Traffic Light
  
  Multiple improvements and new functionalities to enable more and better user assistance via the Traffic Light that is available in front-end applications, such as EPU, Tomography, and MiCo Software.

• Electron Dose Control (EDC)
  
  The beam current prediction is more robust against CFEG flashes, and it better maintains accuracy under CFEG degradation between flashes.

• Biprisms Tool
  
  The new Biprisms Tool allows control of the following properties of up to four biprisms:
  • Voltage and angle stepsize (general info)
  • Holography state (on / off) (general info)
  • Aperture mechanism state for each biprism

The Biprisms tool is available in the Microscope Software Launcher > Tools > Optics menu.

• Bottom-mounted Ceta-2 with Selectris Filter
  
  It is now possible to configure a bottom-mounted Ceta camera with Speed Enhancement (Ceta-2) when a Selectris Energy Filter is present without EF-FalconService camera.
  
  
• Gatan GMS
  
  For embedded cameras and filters, the new GMS 3.5.3.4136 software contains only bugfixes.
  
  For stand-alone cameras and filters, there are some additional functionalities, such as:
  • TruAlign support for the Metro camera.
  • InSitu and secondary camera support for the BioContinuum HD 1067. The BioContinuum HD 1067 with only a K3 camera is supported in embedded configuration. If a secondary camera is added to an embedded BioContinuum HD 1067, then this secondary camera must be configured as a stand-alone camera.

Mid-range TEMs:

• Traffic Light
  
  Multiple improvements and new functionalities to enable more and better user assistance via the Traffic Light that is available in front-end applications, such as EPU, Tomography, and MiCo Software.
  
  
• Alignments and Calibrations
  
  The new Falcon C Detector is supported by the AFIS calibration and by the Optimize Optics SPA sequence.
  
  
• Bottom-mounted Ceta-2 with Selectris Filter
  
  It is now possible to configure a bottom-mounted Ceta camera with Speed Enhancement (Ceta-2) when a Selectris Energy Filter is present without EF-FalconService camera.
  
  
• Gatan GMS
  
  For embedded cameras and filters, the new GMS 3.5.3.4136 software contains only bugfixes.
  
  For stand-alone cameras and filters there are some additional functionalities, such as:
  
  
  • TruAlign support for the Metro camera.
  • InSitu and secondary camera support for the BioContinuum HD 1067. The BioContinuum HD 1067 with only a K3 camera is supported in embedded configuration. If a secondary camera is added to an embedded BioContinuum HD 1067, then this secondary camera must be configured as a stand-alone camera.

Entry level TEMs:

• Traffic Light
  
  Multiple improvements and new functionalities to enable more and better user assistance via the Traffic Light that is available in front-end applications, such as EPU, Tomography, and MiCo Software.
  
  
• Alignments and Calibrations
  
  The new Falcon C Detector is supported by the AFIS calibration and by the Optimize Optics SPA sequence.
  
  
• CryoCycle
  
  The sample count is no longer included in the criteria for the CryoCycle recommendation.

Server software for life sciences

Description of updates

High-end TEMs:

• Optics System
  • When the TEM Server is stopped, the optics boards are no longer shut down. This greatly reduces the time that is needed to stabilize the lenses for high-resolution experiments after the microscope software is started. For supervisor users, the new Microscope Software Launcher (MSL) > Tools > Optics > Recover Optics Boards restores the optics system to working order in case one or more boards have become functionally degraded.
• Alignments and Calibrations
  • When leaving the Column Alignments, all lenses are normalized automatically.
  • The Column Alignments and Direct Alignments for Lorentz Mode (STEM) are improved.
  • On systems with a Holographic Transfer Lens, the nominal and the calibrated magnification values are now adapted for the presence of the Holographic Transfer Lens.
  • AFIS 2.0 calibration brings the following improvements:
    • Autosave: Saves the AFIS calibration to a selected alignment file (*.alg).
    • Validation: Instead of running the entire AFIS calibration procedure, it is now possible to only validate the existing AFIS calibration. The AFIS validation typically takes five to seven minutes.
    • Depending on the system configuration, the AFIS calibration procedure can be completed in 20 to 40 minutes. This is 40% to 60% faster than before.
• Traffic Light
  In addition to Ceta-S and Ceta-F, the Ceta 16M and Ceta-D Cameras are now also supported.
  • The automated User Alignments in MiCo and EPU Software now support Gatan EFTEM filters:
    • Because the location of the Entrance Aperture is not available, the center of the FluScreen is used as a proxy to center the beam.
    • The Optimize Optics sequence is disabled for Gatan filters.
  • In EPU Software, the current alignment file is loaded automatically at the start of User Alignments. In MiCo Software, automatic loading of the alignment file is optional.
  • At the start of the User Alignments, the TMP in the AutoLoader is stopped automatically.
  • The expiration time is increased for most alignments.
    The Find Beam, Beam Center, and Parallel Illumination alignments no longer trigger a recommendation to recover the user alignments. They are automatically executed as the first and last steps every time one of the other alignments is executed.
• EER File Format
  • The metadata of the EER file format is extended with fields to identify the compression scheme.
• Electron Dose Control (EDC)
  
  • The Electron Dose Control (EDC) functionality is now also available on all Spectra 200/300 TEM systems with a CFEG.
• Gatan cameras
  As of TEM Server 7.16.1, the throughput for Gatan cameras that offload their images to a Gatan PC is improved by optimizing the memory footprint of the software components on the Gatan PC.
• STEM
  • On systems with a Probe Corrector and when in Lorentz Mode (STEM), the new Stigmator control panel > Probe A2 function performs threefold condenser stigmation.
• Ultra-X
  • When the new AutoTemperature function is enabled, the Ultra-X detector temperature status follows the system [All Vacuum] state. This causes the sensors to stay cooled while the system can be at room temperature, possibly leading to failures. When disabled, the Ultra-X sensors are kept at room temperature, which is a safe state.
• 4D-STEM

  The minimum dwell-time is restricted to the fastest rate at which no frames will be dropped.

Mid-range TEMs:

• Traffic Light (also known as Tool Readiness)
  • In addition to Ceta-S and Ceta-F, the Ceta 16M and Ceta-D Cameras are now also supported.
  • The automated User Alignments in MiCo and EPU Software now support Gatan EFTEM filters:
    • Because the location of the Entrance Aperture is not available, the center of the FluScreen is used as a proxy to center the beam.
    • The Optimize Optics sequence is disabled for Gatan filters.
  • In EPU Software, the current alignment file is loaded automatically at the start of User Alignments. In MiCo Software, automatic loading of the alignment file is optional.
  • At the start of the User Alignments, the TMP in the AutoLoader is stopped automatically.
  • The expiration time is increased for most alignments. The Find Beam, Beam Center, and Parallel Illumination alignments no longer trigger a recommendation to recover the user alignments. They are automatically executed as the first and last steps every time one of the other alignments is executed.
• Alignments and Calibrations
  • AFIS 2.0 brings the following improvements:
    • Autosave: Saves the AFIS calibration to a selected alignment file (*.alg).
    • Validation: Instead of running the entire AFIS calibration procedure, it is now possible to only validate the existing AFIS calibration. The AFIS validation typically takes five to seven minutes.
    • The AFIS calibration is more robust.
    • Depending on the system configuration, the AFIS calibration procedure can be completed in 20 to 40 minutes. This is 40% to 60% faster than before.
• EER File Format
  • The metadata of the EER file format is extended with fields to identify the compression scheme.
• Gatan cameras
  • As of TEM Server 7.16.1, the throughput for Gatan cameras that offload their images to a Gatan PC is improved by optimizing the memory footprint of the software components on the Gatan PC.
• 4D-STEM
  • The minimum dwell-time is restricted to the fastest rate at which no frames will be dropped.

Entry level TEMs:

• Traffic Light (also known as Tool Readiness)
  • In addition to Ceta-S and Ceta-F, the Ceta 16M and Ceta-D Cameras are now also supported.
  • In EPU Software, the current alignment file is loaded automatically at the start of User Alignments. In MiCo Software, automatic loading of the alignment file is optional.
  • The expiration time is increased for most alignments. The Find Beam, Beam Center, and Parallel Illumination alignments no longer trigger a recommendation to recover the user alignments. They are automatically executed as the first and last steps every time one of the other alignments is executed.
• Cryo Cycle

  The recommended Cryo Cycle intervals are updated:

  • CLS Cryo condition: 10 hours.
  • CLS Room condition: 7 days.
  • TEM (SAL Cryo or Room temperature): 7 days.
• Cryo Loading Station (CLS)
  As of TEM Server 7.16.1, the N2(g) pressure is no longer checked to determine the status of the CLS. If the N2(g) pressure is not OK, then the status of the CLS can still be OK. An incorrect N2(g) pressure does not block normal operation of the CLS.

To obtain update:

Server software for life sciences

Description of updates

High-end TEMs:

• Beam Current and Dose accuracy
  • For Spectra Ultra S/TEM with CFEG, the new BeamCurrentControl calibration brings the following improvements:
  • The accuracy of the predicted the beam current or dose as a function of the selected Gun Lens and Spot Size is improved.
  • The deviation of the actual beam current or dose relative to a requested value is decreased.

For these improvements, the new BeamCurrentControl calibration must be performed by a Thermo Fisher Scientific engineer.

• CFEG
  • When an advice to flash is active, the font color of the TEM User Interface > Status panels > Beam Current changes to orange. After the CFEG is flashed, the font reverts to black.
• Sherpa
  • In APM, the precision, speed, and reliability of the Focus Beam and Stigmate Beam (Condenser Stigmator) is improved.
• Electron Dose Control (EDC)

  When the system is in STEM mode, the Electron Dose Control (EDC) functionality:

  • Allows you to specify the desired beam current or dose. The microscope software automatically adjusts the optics settings to deliver the requested beam current.
  • Predicts the beam current or dose as a function of the selected Gun Lens and Spot Size. In Velox Software, the predicted beam current, dose, and dose rate are displayed at the bottom of the STEM image.
  • Adds the Intensity per pixel to the metadata of STEM images that are acquired in Velox Software with a Panther STEM BF-S or DF-S detector.

  Conditions and restrictions:

  • EDC is only available on Spectra S/TEM systems with a CFEG.
  • EDC is a commercial option.
  • At 30 kV, the accuracy of the EDC functionality is limited.
• STEM

  The STEM Mh Mode option is now available on all Titan TEM systems with STEM.

  
  On Spectra S/TEM systems, Lorentz Mode (STEM) is available.

• CompuStage

  The homing procedure is improved. Before any axis is moved, all axes are checked for error states.

  
  When one or more axes are in an error state, the homing procedure will first attempt recover the error. If recovery fails, the homing procedure will not start.

  
  In preceding software releases the homing procedure would always start and would fail when an axis could not be homed.

• On-System Display (OSD)

  If a displayed tooltip mentions a condition, the tooltip is updated immediately according to the changed condition.

  
  For BSL3 compliant systems, the OSD is automatically shut down when a decontamination heating procedure starts.

Mid-range TEMs:

• CompuStage

  The homing procedure is improved. Before any axis is moved, all axes are checked for error states.

  
  When one or more axes are in an error state, the homing procedure will first attempt recover the error. If recovery fails, the homing procedure will not start.

  
  In preceding software releases the homing procedure would always start and would fail when an axis could not be homed.

• Dual-X

  Dual-X detectors are now supported on Talos F200i TEM with a C-Twin lens.

• Beam Diameter

  The Beam Diameter as displayed in Tomography on Titan TEM systems is now also available on:

  • TEM and EFTEM: Talos F200X TEM, Glacios Cryo-TEM.
  • TEM only: Talos L120C TEM, Tundra Cryo-TEM.

  The accuracy of the calculated Beam Diameter is typically ±20%, but this depends on the accuracy of the Focus and Stigmate alignment and on the selected Spot Size.

• Sherpa
  • In APM, the precision, speed, and reliability of the Focus Beam and Stigmate Beam (Condenser Stigmator) is improved.
  • Align Genie is no longer available in Sherpa. The functionality that was offered via Align Genie is now available in MiCo, except for Talos F200C TEM. On Talos F200C TEM, the Align Genie functionality is now a commercial option.
• On-System Display (OSD)

  If a displayed tooltip mentions a condition, then the tooltip is updated immediately according to the changed condition.

  
  For BSL3 compliant systems, the OSD is automatically shut down when a decontamination heating procedure starts.

Entry level TEMs:

• CompuStage

  The homing procedure is improved. Before any axis is moved, all axes are checked for error states. When one or more axes are in an error state, the homing procedure will first attempt recover the error. If recovery fails, the homing procedure will not start.

  
  In preceding software releases the homing procedure would always start and would fail when an axis could not be homed.

• Sherpa

  Align Genie is no longer available in Sherpa. The functionality that was offered via Align Genie is now available in MiCo.

• Semi Automated Loader (SAL) and Transfer Device (TD)

  In SALSA > Transfer Device, an Exchange widget is available for each attached Transfer Device (TD). In this widget, the new Write data function writes the rough transfer position to the TD.

• On-System Display (OSD)
  • If a displayed tooltip mentions a condition, the tooltip is updated immediately according to the changed condition.
  • For BSL3 compliant systems, the OSD on the TEM is automatically shut down when a decontamination heating procedure starts. The OSD on the CLS remains operational.
• TEM User Interface

  The TEM User Interface can no longer be started by a regular user. Regular users should use MiCo. To gain access to the TEM User Interface, request a supervisor or a Thermo Fisher Scientific engineer to open the Microscope Software Launcher > Tools > Microscope UI Access Provider, enter their credentials and select Provide Access.

To obtain update:
 

Server software for life sciences

Description of updates

High-end TEMs:

• Automated alignments
  • The accuracy and reliability of the automated alignments for SPA image acquisition is improved:
  • Better afterglow detection for the FluScreen and FluCam.
  • Improved robustness of the beam detection and ellipse fitting algorithms.
• Storage Server
  • The connection between the microscope PC and the storage server software is more robust.
• Falcon 4(i) defect masking
  • The default Defect Masking parameters are adjusted so that images can be acquired in a wider dose rate range without visible artifacts.
• Panther STEM BF-S/DF-S
  • On systems with a CFEG, the recorded intensity per pixel (Counts to Electrons) can now be inspected with advanced microscopy image viewers or processing software, such as Velox.
• Dual-X / Single-X
  • The new Bruker Esprit 2.4 software enables multi-user account access to Bruker detectors. Dual-X and Single-X use Bruker XFlash detectors.
• Ultra-X
  • New functionalities to improve the lifetime of the Ultra-X detector:
  • Retract the detector when the column valves are closed.
  • Disable automated cooling of the detector after a defrosting procedure, so the detector can stay at room temperature if the system is not cooled down, for example when an LN2 refill is pending or ongoing.

Mid-range TEMs:

• MiCo
  • MiCo Software is now automatically installed with the TEM Server on Talos L120C G2, Talos F200C G2, Talos Arctica G2, Glacios, and Glacios 2 TEMs.
• Daily Alignments and Optimize Beam functions in MiCo and Traffic Light in EPU
  • The Daily Alignments and Optimize Beam functions in MiCo and the Traffic Light in EPU now support TEM and EFTEM mode.
  • The Daily Alignment and the Optimize Beam functions in Mico and in the EPU Traffic Light are now a full replacement for the AutoAdjust functionality and for the Sherpa APM procedure, provided that:
  • AFIS calibration is completed, and the result is saved in MiCo
  • Starting conditions for the Daily Alignment and the Optimize Beam functions are optimized
  • AutoAdjust functionality is removed from the TEM user interface. Use Align Genie or MiCo instead
  • The Daily Alignment function now supports the 20 μm C2 aperture.
  • Because using the 20 μm aperture results in a significantly lower beam current, the automated procedure can take up to four times longer.
• Automated alignments
• The accuracy and reliability of the automated alignments for SPA image acquisition have been improved:
  • Better afterglow detection for the FluScreen and FluCam
  • Improved robustness of the beam detection and ellipse fitting algorithms

• 30 kV alignment
  • Talos TEM systems can now be aligned at 30 kV.
• Storage server
  • The connection between the microscope PC and the storage server software is more robust.
• Falcon 4(i) defect masking
  • The default defect masking parameters are adjusted so that images can be acquired in a wider dose rate range without visible artifacts.
• Dual-X / Single-X
  • The new Bruker Esprit 2.4 software enables multi-user account access to Bruker detectors. Dual-X and Single-X use Bruker XFlash detectors.

Entry level TEMs:

• Automated alignments
  • The accuracy and reliability of the automated alignments for SPA image acquisition have been improved:
  • Better afterglow detection for the FluScreen and FluCam

Improved robustness of the beam detection and ellipse fitting algorithms.

• Storage Server
  • The connection between the microscope PC and the storage server software is more robust.
• Cryo Loading Station (CLS) and Semi Automated Loader (SAL)
  • The following user actions are added:
  • Abort Go to Room mode
  • Abort Go to Cryo mode
• Tundra User Manuals
  • Tundra Cryo-TEM user manuals are now installed on the microscope PC.

Server software for life sciences

Description of updates

High End TEMs:

• Increased tolerance to pressure spikes in the Octagon
  When a holder is loaded, a short pressure spike can occur. In preceding software releases, the vacuum system immediately stops the IGPco and IGPcl as soon as the pressure exceeds the upper threshold value. To restore operational conditions, the user needs to recover vacuum. Short and small pressure spikes in the octagon are tolerated, they no longer trigger an immediate stop of the column IGPco and IGPcl.
• On System Display (OSD)
  The options for Airlock pumping times on the OSD now match with the TEM User Interface.
• Automated alignments
  The algorithms that are used by multiple automated detection and alignment functions have been improved. This results in faster, more accurate and more reliable automated alignments, and a higher throughput with better quality in (among others) the SPA workflow.
• Sherpa > Customer > OptiSTEM
  When the A1 fine limit is approached, the optimal quality of the OptiSTEM correction can deteriorate. A warning is displayed in the logging panel when the A1 fine limit is approached.
• Storage Server connections
  The RPC connection between the Storage Server on one side, and Thermo Fisher cameras with any type of CMTS on the other side is now more robust.

Mid-Range TEM:

• On System Display (OSD)
  The options for Airlock pumping times on the OSD now match with the TEM User Interface.
• Automated alignments
  The algorithms that are used by multiple automated detection and alignment functions have been improved. This results in faster, more accurate and more reliable automated alignments, and a higher throughput with better quality in (among others) the SPA workflow.
• Align Genie
  The Mh sub-mode, and the LM-STEM and uP-STEM modes are no longer supported in the Align Genie. These modes were introduced as Beta functionality and remain available in the user interface, but they do not meet the required reliability specifications.
• 4D-STEM with Panther STEM
  4D-STEM experiments with Panther STEM detectors are now supported on Talos systems.
• CFEG
  The CFEG is now available for Talos F200i, F200X and F200X G2. Low kV alignments Talos F200i, F200C and F200C G2 now support 30 kV alignments.
• Storage Server connections
  The RPC connection between the Storage Server on one side, and Thermo Fisher cameras with any type of CMTS on the other side is now more robust.

Entry Level TEM:

• Automated alignments
  The algorithms that are used by multiple automated detection and alignment functions have been improved. This results in faster, more accurate and more reliable automated alignments, and a higher throughput with better quality in (among others) the SPA workflow.
• On System Display (OSD)
  The left-side menu now remains available during the execution of a workflow. Sample manipulation actions are now available in the Cassette screen. The guidance for LN2 filling that is displayed when changing to cryo mode is improved.
  When a Cryo Cycle is aborted on the CLS and/or on the TEM, a screen is displayed to inform the user about the 'abort' status.
  The OSD shows a warning when the Semi Automated Loader (SAL) service is not running.
  The Cooldown TEM screen is simplified.
  The Overview and Details tabs are merged into a single Status screen.
  The TEM and CLS images better represent the physical appearance of the equipment.
• MicroProbe at higher magnification
  In MiCo, an HM uP sequence is added for MicroProbe mode in the HM magnification range. This sequence ensures that the system is properly aligned for the Hole/Eucentric Height Preset in EPU.
• Storage Server connections
  The RPC connection between the Storage Server on one side, and Thermo Fisher cameras with any type of CMTS on the other side is now more robust.

To obtain update:
 

Server software for life sciences

Description of updates

High End TEMs:

• Lorentz mode
  When the All lenses zero setting is active, the lens values in the TEM User Interface will now show 0%.
• Falcon 4(i)
  The Falcon 4 and Falcon 4i camera can now also be configured on a system with Monochromator.
• Selectris (X)
  The TEM User Interface now provides more detailed information when the Selectris filter is not operational.
• EMPAD 3S STEM detector
  The EMPAD 3S detector can now be configured in the following positions: Bottom-mounted, on-axis; Filter-mounted or Service hatch.
• NanoMEGAS
  NanoMEGAS can now be enabled in STEM mode.
• Storage Server
  The reliability of the connection with the Storage Server is improved.
  The Traffic Light functionality now also monitors the status of the connection to the Storage Server.
• Collision Prevention
  The collision prevention functionality now blocks simultaneous insertion of the Single-X detector and the Automatic Cryo Box.

Mid-Range TEM:

• Selectris (X)
  The TEM User Interface now provides more detailed information when the Selectris filter is not operational.
• Ceta-F
  The Ceta-F camera is now also supported on Talos L120, F200C and F200i.
• EDS
  Super-X G2 and Super-X G2 Lite are now also supported on Talos F200i. On a system with an EDS detector, it is now possible to configure four Automated Aperture Mechanisms (AAM).
• EMPAD 3S STEM detector
  The EMPAD 3S detector can now be configured in the following positions: Bottom-mounted, on-axis; Filter-mounted, and Service hatch.
• NanoMEGAS
  NanoMEGAS can now be enabled in STEM mode.
• Fringe Free Alignments
  The Fringe Free alignment option is now also available on Talos systems.
• Storage Server
  The reliability of the connection with the Storage Server is improved. The Traffic Light functionality now also monitors the status of the connection to the Storage Server.
• Collision Prevention
  The collision prevention functionality now blocks simultaneous insertion of the Single-X detector and the Automatic Cryo Box.

Entry Level TEM:

• Cryo Cycle
  
  • On the CLS, the conditions for Cryo Cycle recommendation are updated:
    Current temperature: Cryo; Next temperature: Cryo=
    
    • More than 8 hours without Cryo Cycle.
    • More than 9 sample transfers without Cryo Cycle.
    • CLS Pot is opened.
    Current temperature: Cryo; Next temperature: Room temp=
    
    • None
    Current temperature: Room; Next temperature: Cryo=
    
    • More than 3 days in Room Temperature mode.
    • The CLS is used:
      • Standby mode is interrupted.
      • A sample transfer is started.
      • The Transfer Device is docked or undocked.
      • The CLS Pot is opened.
    Current temperature: Room; Next temperature: Room=
    • More than 7 days without Cryo Cycle.
  • The OSD now uses three separate screens to guide the user through the Cryo Cycle procedure: two screens for preparation, followed by one screen for the execution of the Cryo Cycle.
  • The default Cryo Cycle duration is changed to 480 minutes.
  • The estimated remaining time for a Cryo Cycle now depends on the LN2 level. This makes the estimation more accurate.
  • An ongoing Cryo Cycle on the TEM or the CLS no longer locks the OSD on the other unit. This makes it possible to simultaneously perform a Cryo Cycle on the TEM and on the CLS.
• Temperature Control
  The OSD now shows the temperature status of the CLS and the TEM.
  And an animated guide how to refill the LN2 Dewar on the TEM.
  The Go to Cryo procedure can be stopped after the LN2 level has reached OK. It is no longer necessary to wait until the LN2 Dewar is completely filled before starting the sample manipulation actions.
• Sample Transfer
  If a sample transfer is started while a Cryo Cycle is recommended on the CLS and/or the TEM, then a warning is displayed that requests the user to start the Cryo Cycle. It is possible to ignore the warning and resume the sample transfer procedure without performing a Cryo Cycle.
  The OSD now shows a progress bar for the current status and progress of the sample transfer between the CLS and the TEM.
  The LED strip on the CLS indicates the status of the Transfer Device (TD):
  • On: TD is connected, no action needed.
  • Blinking: insert or remove the TD.
  • Off: TD is not connected, no action need.
• Storage Server
  The reliability of the connection with the Storage Server is improved. The Traffic Light functionality now also monitors the status of the connection to the Storage Server.
• Error Recovery
  The error handling and recovery functions on the TEM and on the CLS are significantly extended and improved.
  The OSD on the TEM now shows a button to recover from an error condition.
  After the emergency stop (EMO) is pressed on the CLS, the OSD on the CLS shows instructions how to bring the CLS back to an operational state.
  After a recovery procedure on the CLS, the Cryo or Room temperature mode is determined as follows:
  
  • If the LN2 level is above Critical level, then the CLS goes to Cryo mode.
  • If the LN2 level is between Critical and Empty, then the CLS goes to Error mode and requests the user to select the desired temperature mode.
  • If the LN2 level is Empty, then the CLS goes to Room temperature mode.

To obtain update:
 

Server software for life sciences

Description of updates

Source and HT:

• On titan systems, the High-T flash button in CFEG control > Expert flap-out is removed. Instead, the system automatically assigns the most suitable flashing function (either Low-T or High-T flash) to the Flash button.

Vacuum:

• For systems with a Titan Basic G2.0 vacuum system, the Vacuum control panel > Settings > Airlock pump time options list is extended with 900, 1200, 1500 and 1800 seconds.

Optics:

• The automated Sherpa > AFIS alignment is now also available on Talos F200C.

Cameras, filters, and detectors:

• Falcon 4i is now also available as a bottom-mounted camera on Talos F200i and F200S.
• To prevent damage to the sensor of a Falcon 4 or Falcon 4i camera during continuous acquisition, the beam will be blanked when: 
  • The magnification changes. 
  • The magnification range changes (LM <> HM). 
  • The probe mode changes (MicroProbe <> Nanoprobe).
• Sherpa > Energy Filter: The automated Crossover Correction tuning is now available for Supervisor users.
• Ceta-F is now also available on Talos F200i and L120C.
• EMPAD. The metadata in the image file is extended with additional parameters: PixelSize, DiffractionPatternRotation, and ImageRotation.

Motion and Sample Loaders:

• WARNING: The CryoCycle procedure now uses target temperatures instead of a timer: 
  • Autoloader: docker temperature exceeds 228 K 
  • Column: holder temperature exceeds 280 K
• After a CryoCycle, the following Temperature Control states are available: 
  • All Nitrogen Temperature: Temperature Control will put the system to All Nitrogen Temperature state immediately after the CryoCycle is completed. 
  • All Nitrogen Temperature delayed: Temperature Control will put the system to All Nitrogen Temperature state at the specified date and time. 
  • All Room Temperature delayed: Temperature Control will put the system to All Room Temperature state at the specified date and time. This state is only available after a CryoCycle of both the Column and Autoloader.

All items below are applicable for Tundra systems:

• The heater on the LN2 Dewar in the Tundra system now has a configurable maximum temperature with a configurable margin, so that all LN2 can evaporate without overheating the Dewar.
• Semi-Automated Loader (SAL)
• The Exchange Position Wizard is now available, including motor calibration.
• The LED Matrix on the Tundra indicates the status of the SAL: 
  • Blue: OK. 
  • Blinking blue: OK, exchange is ongoing. 
  • Red: Not OK. 
  • An emergency stop button (EMS) is available. When pushed, the ongoing exchange is aborted, and the Cryo Loading Station (CLS) reverts to a standby status. Recovery of the EMS status is guided via the On System Display (OSD).
• On System Display (OSD): 
  • Guidance is added for the execution of a Cryo Cycle, including how to bring the Tundra system to a cryogenic temperature status. 
  • Maintenance screens: A function is added to manually detach the transfer device and a guidance is added to refill the LN2 Dewar on the CLS.

Server software for life sciences

Description of updates

• Support for the Thermo Scientific Falcon 4i Detector on all systems that support its predecessor, the Falcon 4 Detector.
• The Falcon 4i Detector is available as a BM and an EF camera.

Server software for life sciences

Description of updates

• On systems with a Thermo Scientific Selectris (X) filter, the EFTEM lens series are revised. After a software upgrade from TEM Server 7.8.X or earlier, all EFTEM alignments and all EFTEM magnification calibrations must be renewed for all high-tension voltages.
• The Gatan US1000XP, OneView, or Continuum NR cameras have moved from the GCI2 interface to the faster and more stable GatanRpcServer interface

Server software for life sciences

Applicable instruments

• (Titan) Krios with Windows 10

Description of updates

• It is now possible to configure two Falcon 4 cameras on a single system: one in bottom-mounted position (BM) and one in energy filter position (EF).
• Advanced TEM Scripting additions:
  • AutoLoader functions
  • Temperature Control functions
  • Selectris Slit control functions
• Krios
  • The Focus Stigmator calibration is now available in Sherpa, enabling AutoCTF and 3-fold asigmatism correction.
  • The Magnification Calibration for Krios systems is now based on the oriented gold specimen instead of the cross-grating specimen. This results in a higher accuracy of the 3D reconstructions.
     
• Glacios / Talos dose impact
  • With R2.7.1, a new spot sizes series is introduced

• With the original spot sizes series, screen current fluctuates within 35–85% when changing the spot size. For better predictability a new spot size series is introduced which keeps the screen current fluctuation within 50–60%.
• Due to the changed spot size series, each spot size value will result in a different dose on the camera compared with the previous TEM server versions.
• When unchanged dose on the camera is desired, session parameters need to be adjusted accordingly. In order to recover the same dose on the camera it may be required to change spot size and gun lens values.

Availability:

• Included in service contracts
• Windows 7 to Windows 10 commercial upgrades are available as Non Standard Request (NSR) for Glacios/Talos and (Titan) Krios

Server software for life sciences

Applicable instruments

• (Titan) Krios with Windows 10

Description of updates

• Source and High Tension:
  • CFEG: Supported by the Ice Growth microscope test.
  • CFEG: The Smart BCM based ramping algorithm is now available for the High Temperature flash procedure.
• Vacuum:
  • The Vacuum Analyzer replaces the obsolete Pressure Logger.
• Optics:
  • The CEOS Corrector software and user interfaces now support the following Gatan filters:
    • Gatan Continuum 1069 Dual with K3 camera.
    • Gatan BioContinuum 1067 with K3 camera.
• Cameras and Detectors:
  • EMPAD 3S: Allows stand-alone 3rd party STEM detectors to synchronize with the Panther STEM CAB/A scan engine.
  • 4D STEM with Ceta-2: The pixels in the first column of the camera sensor are no longer over-exposed.
  • Gatan GMS: The software interface with Gatan Digital Micrograph now supports Dose Protector events for the following Gatan filters:
    • Continuum 1069 with K3
    • BioContinuum 1067 with K3
    • BioQuantum 1967 with K3
    • BioQuantum 967/968 with K2
  • Gatan GMS: The following applications and processes can now be executed with regular user privileges. It is no longer necessary to use the Run as Administrator option:
    • The GMS application.
    • RpcServer (started automatically) for all configurations with a BioQuantum 1967 or Continuum 1067 filter and the Gatan camera is shipped with a dedicated Gatan PC.
    • GfiRemoteProxy (started automatically) for all system configurations where the Gatan camera is shipped with a dedicated Gatan PC.
• Motion and Autoloader:
  • Autoloader TMP: Recovery function automatically recovers TMPAL errors on the Autoloader. If recovery fails, then a message is displayed and a new UEC is logged.
  • Piezo Controller: New firmware must be uploaded to the Piezo controller. If the Piezo controller is powered on and connected, then the firmware is uploaded automatically during the TEM Server installation. If not, then the firmware can be uploaded manually via TAD.

Availability:

• Included in service contracts
• Windows 7 to Windows 10 commercial upgrades are available as Non Standard Request (NSR) for Glacios/Talos and (Titan) Krios

Server software for life sciences

Applicable instruments

• Glacios, Talos and (Titan) Krios (requires Windows 10)

Description of updates

• For all systems with an Autoloader and/or a Falcon 4 camera, it is strongly recommended to upgrade because of a critical bug fixes
• Source and High Tension: o CFEG
  • The new smart Beam Current Measurement (BCM) based ramp up function ensures stable beam currents after a low temperature flash.
  • CFEG: The timestamp of the most recent CFEG Flash is added to the metadata parameters in the MRC2014 FEI2 Extended Header image format.
  • CFEG: CFEG is now also available for Metrios AX 4.0.
  • Sherpa: HT Conditioning tool which supersedes standalone TEM FEG Auto Alignment Software
• Optics
  • Falcon 4 Pro-active Protector: The range of the Falcon 4 Pro-active Protector is extended with High Tension voltages below 200 kV.
  • Sherpa > APM: The following procedures are automated:
    • Condenser center TEM
    • Condenser stigmation
  • OptiSTEM+:
    • Improved feedback with user guidance when the procedure fails.
    • The A2 and B2 procedures can now be executed separately.
    • The new B2/A2 single shot function executes one iteration of the procedure. On bad specimens, this function gives the user the more control to optimize the system step-by-step.
• Cameras and Detectors
  • Selectris and Selectris X: The Thermo Scientific Selectris and Thermo Scientific Selectris X Energy Filters are introduced for Krios and Glacios microscopes.
  • Falcon 4:
    • Continuous Acquisition (Live Mode) is available for the factory account. Continuous Acquisition streams the live image to TIA.
    • Advanced Scripting now supports EER acquisition.
  • Flucam Viewer: A new overlay is available with a 360 degree scale.
  • Gatan Continuum with K3: The Duty Cycle setting is now supported. This allows for shorter exposure times (< 0.0133 sec), which leads to better results for the Monochromator auto-tuning procedure on a system with UltiMono.
• Motion and Autoloader
  • OSD: New functions on the On-System Display (OSD) for Krios G4:
    • Load Cartridge can now be done in one step.
    • The Cassette Slot status (empty / filled) is now displayed.

Availability:

• Included in service contracts
• Windows 7 to Windows 10 commercial upgrades are available as Non Standard Request (NSR) for Glacios/Talos and (Titan) Krios

Server software for life sciences

Applicable instruments

• Glacios, Talos and (Titan) Krios with Windows 10

Description of updates

• (Titan) Krios, Source and High Tension: Support for CFEG beam current stability optimization routines to condition the tip before first use.
• (Titan) Krios, Vacuum: IGP2CI power supply support
• Optics:
  • Added the Camera to Camera calibration FluCam in Sherpa.
• Cameras and Detectors:
  • Falcon 4: The Gain Reference image for EER acquisitions is now stored as a TIFF file on the Storage Server to support EPU Quality Monitor (EQM) and 3rd party image processing applications.
  • Falcon 4: CMTS-based Qualification Tool for Sensor Package qualification.
  • Falcon 4: camera is now also available for Talos F200C systems
  • Gatan Continuum: The Gatan BioContinuum filter is now supported in embedded configuration.
  • Gatan Continuum: Embedding is now available for systems shipped stand alone. See WI 308947 for details.
  • Gatan Continuum: It is now possible to align the corrector with the post-filter camera of a Gatan Continuum 1065/1066 filter, provided that the camera is available as EF-CCD in the CCD/TV Camera control panel.
  • Gatan Continuum: For a Gatan Continuum dual-camera filter only the camera that is configured as EF-CCD can be used for corrector alignment.
  • Gatan K3: Forced defect correction is now supported for uncorrected counting / super resolution acquisitions. This correction allows for valid dark corrected fractions for post-processing clients.
  • FluCam: The FluCam image is now available on the On System Display (OSD)

Availability:

• Included in service contracts
• Windows 7 to Windows 10 commercial upgrades are available as Non Standard Request (NSR) for (Titan) Krios

Server software for life sciences

Applicable instruments

• Krios G3 with Windows
• Krios G3i Cryo-TEM with Windows 10
• Krios G4 Cryo-TEM with Windows 10

Description of updates

• For HT Tank G2.3, fast ramping is now available on systems with a corrector
• Camera to Camera calibration now supports the FluCam in combination with the Ceta camera
• Falcon 4: Drift Corrected Frame Integration (DCFI) is now supported for drift up to 50 px/s
• For the Gatan BioQuantum with K3 camera, the CDS mode is now supported in embedded configuration
• For Gatan BioQuantum with K3 camera cameras, Dark Reference image can be made (via EPU and Tomography)

Availability:

• Included in service contracts
• Windows 7 to Windows 10 commercial upgrades are available as Non Standard Request (NSR) for (Titan) Krios

Server software for life sciences

Applicable instruments

• Krios G3
• Krios G3i Cryo-TEM
• Krios G4 Cryo-TEM

Description of updates

• Falcon 4 now supports Electron Event Registration (EER) and Integration Mode
• Gatan Continuum S1077 is now available as an embedded filter
• Ultimono is automatically disabled after 3 days to prevent emitter deterioration and long recovery times
• Sherpa
  • OptiSTEM now supports systems with XFEG and with X-CFEG sources
  • OptiMono now supports Gatan Continuum filters
  • OptiMono+ extends the regular OptiMono functionality to Ultimono conditions

Availability:

• Included in service contracts

Server software for life sciences

Applicable instruments

• Krios G3
• Krios G3i Cryo-TEM
• Krios G4 Cryo-TEM

Description of updates

• The Falcon 4 camera is available in bottom-mounted configuration, only in combination with a Ceta camera
• Extended Drift Correction is now available for Falcon 3EC cameras
• When High Tension switches off, the Lensref no longer scales down
• Dose Protection for Falcon 4 on systems with a CEOS corrector
• New automatic alignments
  • The manual Rotation Center alignment is replaced by an automated version
  • Center Objective Aperture: Accuracy is improved from a reasonable centered aperture to a perfectly centered aperture
  • Rotation Center Alignment:
    • Automated version is now available for Talos systems
    • Increased speed and robustness
  • Presets for EFTEM mode:
    • Use counting mode instead of linear mode
    • Use align integrated image
    • Use spot size 7 or 8, depending on alignment

Availability:

• Advanced TEM scripting is free-of-charge, but must be activated via our On-Site software update service

Server software for life sciences

Applicable instruments

• Glacios/Talos and (Titan) Krios with Windows 7

Description of updates

• Last W7 (maintenance) release! This is the recommended release for all Windows 7 systems.
• For all systems with an Autoloader and/or Falcon 4 camera, it is strongly recommended to upgradeto Windows 10

Availability:

• Included in service contracts
• Windows 7 to Windows 10 commercial upgrades are available as Non Standard Request (NSR) for (Titan) Krios

Server software for life sciences applications

Applicable instruments

• Krios G4 Cryo-TEM

Description of updates: 2.15.1, 2.15.2

• Titan 2.15.1: No embedding for BioQuantum-K3
• Titan 2.15.2: Embedding for BioQuantum-K3
• Embedding for Ceta-D camera
• Advanced TEM scripting
• Automated Performance Monitoring (APM): The Objective aperture precondition for the Center Objective Aperture alignment is changed from the 70 µm to the 100 µm aperture
• Aberration Free Image Shift (AFIS), which enables EPU to achieve a higher throughput
• Automatic Cryo-cycle for systems with an Autoloader

Availability

• Titan 2.15.1: Does not support BioQuantum-K3
  
• Titan 2.15.2: Only runs if BioQuantum-K3 is presentIncluded in service contracts
• The AFIS calibration must be done by a Thermo Fisher Scientific engineer
• Advanced TEM scripting is free-of-charge, but must be activated via our On-Site software update service

Server software for life sciences applications

Applicable instruments

• Krios G3i Cryo-TEM

Description of updates

• Advanced TEM scripting (Extended scripting interface for academic third-party data acquisition software)
  
  • Falcon 3EC (counting mode) support
  • Interface to switch to next phase plate position

• Automated Permance Monitoring (APM)
  • The objective aperture precondition for the center objective aperture alignment is changed from the 70 µm to the 100 µm aperture

Availability

• This software release only supports Advanced TEM scripting on Krios G3i. Other platforms will be supported later (expected in June 2019 for all Krios platforms)
• Titan 2.14.1 shall only support APM on Krios G3i systems
• Included in service contracts

Server software for life sciences

Description of updates

• Support for the Thermo Scientific Falcon 4i Detector on all systems that support its predecessor, the Falcon 4 Detector.
• The Falcon 4i Detector is available as a BM and an EF camera.

Server software for life sciences

Description of updates

• On systems with a Thermo Scientific Selectris (X) filter, the EFTEM lens series are revised. After a software upgrade from TEM Server 7.8.X or earlier, all EFTEM alignments and all EFTEM magnification calibrations must be renewed for all high-tension voltages.
• The Gatan US1000XP, OneView, or Continuum NR cameras have moved from the GCI2 interface to the faster and more stable GatanRpcServer interface

Server software for life sciences

Applicable instruments

• Talos and Glacios systems with Windows 10

Description of updates

• Source and High Tension:
  • CFEG: Supported by the Ice Growth microscope test.
  • CFEG: The Smart BCM based ramping algorithm is now available for the High Temperature flash procedure.
• Vacuum:
  • The Vacuum Analyzer replaces the obsolete Vacuum Logger.
  • The IGP Cable disconnect timeout is decreased from 5 minutes to 15 seconds.
  • The TEM HAL dialog (tstHalNG) has a new Vacuum-only profile.
  • The Vacuum service dialog has a new notification about waiting 15 minutes for Falcon 4.
• Optics:
  • Align Genie new alignments:
    • Center C2 (STEM nP Imaging mode).
    • Beam Tilt Pivot Points (STEM nP Imaging mode).
    • Condenser Stigmation (STEM nP Imaging mode).
    • Set Eucentric Height (cross-grating in TEM uP).
• Cameras and Detectors:
  • EMPAD 3S: Allows stand-alone 3rd party STEM detectors to synchronize with the Panther STEM CAB/A scan engine.
  • 4D STEM with Ceta-2: The pixels in the first column of the camera sensor are no longer over-exposed.
  • Gatan GMS: The software interface with Gatan Digital Micrograph now supports Dose Protector events for the following Gatan filters:
    • Continuum 1069 with K3
    • BioContinuum 1067 with K3
    • BioQuantum 1967 with K3
    • BioQuantum 967/968 with K2
  • Gatan GMS: The following applications and processes can now be executed with regular user privileges. It is no longer necessary to use the Run as Administrator option:
    • The GMS application.
    • RpcServer (started automatically) for all configurations with a BioQuantum 1967 or
    • Continuum 1067 filter and the Gatan camera is shipped with a dedicated Gatan PC.
    • GfiRemoteProxy (started automatically) for all system configurations where the Gatan camera is shipped with a dedicated Gatan PC.
• Motion and Autoloader:
  • Autoloader TMP: Recovery function automatically recovers TMPAL errors on the Autoloader. If recovery fails, then a message is displayed and a new UEC is logged.
  • Piezo Controller: New firmware must be uploaded to the Piezo controller. If the Piezo controller is powered on and connected, then the firmware is uploaded automatically during the TEM Server installation. If not, then the firmware can be uploaded manually via TAD.
     
• Glacios / Talos dose impact
  • With R2.7.1, a new spot size series is introduced

• With the original spot size series, screen current fluctuates within 35–85% when changing the spot size. For better predictability a new spot size series is introduced which keeps the screen current fluctuation within 50–60%.
• Due to the changed spot size series, each spot size value will result in a different dose on the camera compared with the previous TEM server versions.
• When unchanged dose on the camera is desired, session parameters need to be adjusted accordingly. In order to recover the same dose on the camera it may be required to change spot size and gun lens values.

Availability:

• Included in service contracts
• Windows 7 to Windows 10 commercial upgrades are available as Non Standard Request (NSR) for Glacios/Talos and (Titan) Krios

Server software for life sciences

Applicable instruments

• Glacios, Talos and (Titan) Krios (requires Windows 10)

Description of updates

• For all systems with an Autoloader and/or a Falcon 4 camera, it is strongly recommended to upgrade because of a critical bug fixes
• Source and High Tension: CFEG
  • The new smart Beam Current Measurement (BCM) based ramp up function ensures stable beam currents after a low temperature flash.
  • CFEG: The timestamp of the most recent CFEG Flash is added to the metadata parameters in the MRC2014 FEI2 Extended Header image format.
  • CFEG: CFEG is now also available for Metrios AX 4.0.
  • Sherpa: HT Conditioning tool which supersedes standalone TEM FEG Auto Alignment Software
• Optics:
  • Falcon 4 Pro-active Protector: The range of the Falcon 4 Pro-active Protector is extended with High Tension voltages below 200 kV.
  • Sherpa > APM: The following procedures are automated:
    • Condenser center TEM
    • Condenser stigmation
  • OptiSTEM+:
    • Improved feedback with user guidance when the procedure fails.
    • The A2 and B2 procedures can now be executed separately.
    • The new B2/A2 single shot function executes one iteration of the procedure. On bad specimens, this function gives the user the more control to optimize the system step-by-step.
• Cameras and Detectors:
  • Selectris and Selectris X: The Thermo Scientific Selectris and Thermo Scientific Selectris X Energy Filters are introduced for Krios and Glacios microscopes.
  • Falcon 4:
    • Continuous Acquisition (Live Mode) is available for the factory account. Continuous Acquisition streams the live image to TIA.
    • Advanced Scripting now supports EER acquisition.
  • Flucam Viewer: A new overlay is available with a 360 degree scale.
  • Gatan Continuum with K3: The Duty Cycle setting is now supported. This allows for shorter exposure times (< 0.0133 sec), which leads to better results for the Monochromator auto-tuning procedure on a system with UltiMono.
• Motion and Autoloader:
  • OSD: New functions on the On-System Display (OSD) for Krios G4:
    • Load Cartridge can now be done in one step.
    • The Cassette Slot status (empty / filled) is now displayed.

Availability:

• Included in service contracts
• Windows 7 to Windows 10 commercial upgrades are available as Non Standard Request (NSR) for Glacios/Talos and (Titan) Krios

Server software for life sciences

Applicable instruments

• Glacios, Talos and (Titan) Krios with Windows 10

Description of updates

• (Titan) Krios, Source and High Tension: Support for CFEG beam current stability optimization routines to condition the tip before first use.
• (Titan) Krios, Vacuum: IGP2CI power supply support
• Optics:
  • Added the Camera to Camera calibration FluCam in Sherpa.
• Cameras and Detectors:
  • Falcon 4: The Gain Reference image for EER acquisitions is now stored as a TIFF file on the Storage Server to support EPU Quality Monitor (EQM) and 3rd party image processing applications.
  • Falcon 4: CMTS-based Qualification Tool for Sensor Package qualification.
  • Falcon 4: camera is now also available for Talos F200C systems
  • Gatan Continuum: The Gatan BioContinuum filter is now supported in embedded configuration.
  • Gatan Continuum: Embedding is now available for systems shipped stand alone. See WI 308947 for details.
  • Gatan Continuum: It is now possible to align the corrector with the post-filter camera of a Gatan Continuum 1065/1066 filter, provided that the camera is available as EF-CCD in the CCD/TV Camera control panel.
  • Gatan Continuum: For a Gatan Continuum dual-camera filter only the camera that is configured as EF-CCD can be used for corrector alignment.
  • Gatan K3: Forced defect correction is now supported for uncorrected counting / super resolution acquisitions. This correction allows for valid dark corrected fractions for post-processing clients.
  • FluCam: The FluCam image is now available on the On System Display (OSD)

Availability:

• Included in service contracts
• Windows 7 to Windows 10 commercial upgrades are available as Non Standard Request (NSR) for (Titan) Krios

Server software for life sciences

Applicable instruments

• Glacios Cryo-TEM with Windows 10
• Talos Arctica TEM with Windows 10

Description of updates

• Align Genie: Added the following alignments:
  • Align Rotation Center
  • All LM Magnifications
• The 100 kV alignment is now available for Talos F200i
• The SP Twin Lens is now supported
• Falcon 4 is now available for Talos systems in Standard mode
• For the Gatan BioQuantum with K3 camera, the CDS mode is now supported in embedded configuration
• For Gatan BioQuantum with K3 camera cameras, Dark Reference image can be made (via EPU and Tomography)

Availability:

• Included in service contracts

Server software for life sciences

Applicable instruments

• Glacios Cryo-TEM
• Talos Arctica TEM

Description of updates

• (Sherpa > Spot Saturation) automatically optimizes gun tilt and filament heating to maximize the beam current and optimize the shape of the spot, without overheating the filament. Spot Saturation is only available for systems with a LaB6 source.
  
• The Vacuum Analyzer replaces the obsolete Vacuum Logger too.
• The Vent All action is automated.

Availability:

• Included in service contracts

Server software for life sciences

Applicable instruments

• Glacios Cryo-TEM
• Talos Arctica

Description of updates:

• The Falcon 4 camera is available in bottom-mounted configuration, only in combination with a Ceta camera
• Extended Drift Correction is now available for Falcon 3EC cameras
• When High Tension switches off, the Lensref no longer scales down
• Dose Protection for Falcon 4 on systems with a CEOS corrector
• New automatic alignments
  • The manual Rotation Center alignment is replaced by an automated version
  • Center Objective Aperture: Accuracy is improved from a reasonable centered aperture to a perfectly centered aperture
  • Rotation Center Alignment:
    • Automated version is now available for Talos systems
    • Increased speed and robustness
  • Presets for EFTEM mode:
    • Use counting mode instead of linear mode
    • Use align integrated image
    • Use spot size 7 or 8, depending on alignment

Availability:

• Advanced TEM scripting is free-of-charge, but must be activated via our On-Site software update service

Server software for life sciences

Applicable instruments

• Glacios/Talos and (Titan) Krios with Windows 7

Description of updates

• Last W7 (maintenance) release! This is the recommended release for all Windows 7 systems.
• For all systems with an Autoloader and/or Falcon 4 camera, it is strongly recommended to upgradeto Windows 10

Availability:

• Included in service contracts
• Windows 7 to Windows 10 commercial upgrades are available as Non Standard Request (NSR) for (Titan) Krios

Server software for life sciences applications

Applicable instruments

• Glacios Cryo-TEM
• Talos Arctica TEM
  

Description of updates

• Advanced TEM scripting
• Automated Performance Monitoring (APM): The Objective aperture precondition for the Center Objective Aperture alignment is changed from the 70 µm to the 100 µm aperture
• Automatic Cryo-cycle for systems with an Autoloader

Availability

• Talos 1.15.1: Does not support BioQuantum-K3 (will be available in Talos 1.15.2)
• Included in service contracts
• Advanced TEM scripting is free-of-charge, but must be activated via our On-Site software update service

Server software for life sciences applications

Applicable instruments

• Glacios Cryo-TEM

Description of updates

• Automated Performance Monitoring (APM)
  
  • New function that assesses the microscope alignment status in a semi-automated fashion

Availability

• Included in service contracts
• Advanced TEM scripting is not yet supported in this release, but is expected to become available starting with the Talos 1.15 software update (July 2019) for Glacios/Talos platforms

Description of updates

• CryoFlow introduction: Tomo Live is enabled by the new CryoFlow Software, which serves as a successor to Athena Software.
  
  
• Parallelization for Search Maps Definition: Users can create a new Tomography session and define Search Maps during Atlas acquisition/screening.
  
  
• Some parameters of Auto Eucentric are automatically pre-defined for the user during Search Map Queue acquisition
  To ensure the optimal running of Search Map queue acquisition, Auto Eucentric uses the LM preset for rough steps only before the first Search Map. Any other Auto Eucentric then skips the LM rough step. Between each Auto eucentric, the Z height is not reset to 0.

Watch this tutorial to learn how about the latest capabilities in Tomography software 5.19

Download release notes for Tomography Software 5.19

Compatibility: Titan SW 3.16.x – 3.21.x / Talos SW: 2.16.x – 2.21.x. 

Tomography software

Description of updates

• Batch positions can be defined while the tilt series is running
  
  The newly defined batch positions are automatically acquired in the order specified in the list.
  You are able to edit defocus and add comments while the tilt series is running.
  
  
• Lamella Option in Session setup 
  
  A new Lamella option has been added to the Tomography session. This option provides functionality related to the Lamella use case, including Maps TEM AutoSync and defining lamella orientation.
  You will receive a warning if the lamella orientation is missing.
  
  
• Editing batch positions on Search Maps 
  
  You are able to edit the positions of template areas (excluding the primary exposure area) on the Search Map. Targeted single acquisition.

Release notes

Compatibility: Titan SW 3.15.x – 3.20.x / Talos SW: 2.15.x – 2.20.x. 

Tomography software

Description of updates

• Targeted single acquisition
  
  Targeted single acquisition is possible in Tomo on Slab like samples in Batch mode, it can be activated in the Acquisition flap out as a Beta feature. During Targeted single acquisition, automatic acquisition is executed only on the start angle.
  
  
• Data Exchange with Maps TEM is possible for systems with Maps TEM installed. The following data can now be automatically synchronized between both applications:
  
  • Annotations created in Maps, including sites of interest, areas of interest, and lamella information.
  • Batch positions created in Tomography, including exposure, tracking, focus, and condition areas.

Release notes

Compatibility: Titan SW 3.14.x – 3.19.x / Talos SW: 2.14.x – 2.19.x.  

Tomography software

Description of updates

• Improving predictive tracking
  
  Tracking of multi-shot exposure areas off-axis has been significantly improved. Multi-shot acquisition can now be reliably used on samples that are not perfectly flat and on features don't shift during acquisition of off-axis areas.
  
  
• Improved interaction with Search Maps
  
  Defining and editing of Search Maps is easier and more convenient, as position and size of the queued search maps can be edited.
  
  
• Set up TomoLive Software runs outside the Athena Software portal
  
  It is now possible to create folders and workflows in Tomo 5 Software, without using the Athena Software portal.

Release notes

Compatibility: Titan SW 3.13.x – 3.18.x / Talos SW: 2.13.x – 2.18.x. 

Tomography software

Description of updates

• Compression for Data Acquisition Images:
  • On systems with a Falcon 4i Detector, you can enable LZW Compression for Data Acquisition images at Preparation > Exposure Settings > Compression. The compression is applied on Data Acquisition images stored in TIFF at native 4k x 4k resolution.
  • This feature uses non-gain-normalized compression.
  • To activate this feature, set Fractions to manual or max, specify the number of fractions desired, and set Compression to Yes.
  • Note: Requires TEM Server 7.17 (Titan 3.17 / Talos 2.17)
• Gain Reference Copy for EER or TIFF Output: When using a Falcon 4I Detector and EER or TIFF as output for the data acquisition preset, a copy of the gain reference is now supplied in the folder containing the movies.
• Load Tomography session: Users can now load existing Tomography Software sessions, which contain experiment settings, Athena Software settings, output settings, email settings, and data saved in the corresponding storage folder.

Compatibility: Titan Cryo-TEM SW 3.12.x – 3.17.x / Talos TEM SW: 2.12.x – 2.17.x.

Tomography software

Description of updates

• Work with Screened Atlases without Loading on Stage.
  • You can now view and select an acquired Atlas in the Tomo tab within the new Sample workflow step to prepare your experiment.
  • No need to load the Atlas on stage.
  • Initiating a queue of Search Maps on an Atlas not loaded on stage will automatically trigger the load.
  • To work on a different screened Atlas, simply create a new Tomo session and proceed with Search Maps definition.
  • This feature is available only for systems equipped with an autoloader.
• Autofocus settings used during Optimized position calibration in STEM can be changed in Autofunctions → Autofocus Linear. The calibration process utilizes the Autofocus Linear settings specified by the user.
• Movie Player in Tilt Series in Batch Mode: Dramatically improved the loading speed of movies by using saved thumbnails.
  • The loading speed has been significantly improved for all image sizes, providing a better user experience.
  • For the 4k x 4k image size, the improvement is even more substantial with 20 times faster loading speed, reduced from 20 seconds to just 1 second.
• Search Maps acquired as part of a Queue now display a highlighted Z height, indicating that they have been acquired at Eucentric height. Additionally, all images acquired using the Move Stage here and Acquire function on a Search Map at Eucentric height will also be highlighted.
• The default path for data storage is drive D (if available).
• MicroProbe STEM Option Hidden for Unsupported Systems.
  • The MicroProbe STEM option is now hidden in the interface for microscope systems that do not have the MicroProbe STEM hardware configuration, making the interface cleaner.

Compatibility: Titan TEM SW 3.11.x – 3.16.x / Talos TEM SW: 2.11.x – 2.16.x.

Tomography software

Description of updates

• Optics settings of high SA presets can be linked to the Exposure preset. Parameters of the Optics settings that can be linked are the ProbeMode, Magnification, Spot Size, Illuminated Area, Intensity, Insert Slit, and Slit Width.
• The LZW compression feature is temporarily removed.
• Auto Functions tab: For each Auto Function task, Tomography now selects the relevant preset automatically. For example, the Autofocus preset is automatically selected for the Autofocus task.
• Acquisition and Optics Settings task: The ribbon is now much cleaner. Some redundant parameters have been removed from the user interface; other parameters have been moved from the main ribbon into expandable trays.
• The default path for data storage is drive D (if available).

Compatibility: Titan SW 3.10.x – 3.15.x / Talos SW: 2.10.x – 2.15.x. 

Tomography software

Description of updates

• Calibrations for more accurate targeting of identifiable features during automated Data Acquisition. It also improves the alignment between tiles of Atlas and Search Map images.
• Dose Symmetric group sizes of 2, 3 and 4.
• Trigger ZLP Adjustment and Phase Plate Activation every Nth tilt series.
• A measurement tool for the Image Display.
• A Lamella orientation tool is introduced to measure distances on the Image Display.

To obtain update: 

Description of updates

• Tilt series can be reconstructed into tomograms using Tomo Live for easier review and quality control.
• Reconstructed datasets can be viewed anywhere using our web-based portal supported by Athena.
• Dataset filtering based on certain parameters and/or manual rating.
• Reconstruction exporting in batches ready for segmentation and processing.
• Additional Exposure Areas in the Batch Position template can now be defined off-axis.
• Multiple Search Maps can now be acquired automatically and unattended
• Support for Ceta-F camera, as well as compressed TIF on Falcon 4(i) cameras.

To obtain update: 

Tomography software

Description of updates

• Batch positions can be defined on previously acquired Search Maps, for easier and faster set-up.
• Previously defined batch positions can be edited before the position is refined.
• [Beta] Multiple exposure areas on the tilt axis can be added to each batch position, for faster acquisition.
• An additional high magnification centering step has been added for single tilt series with large start angles to improve targeting accuracy.
• EDS images can be acquired at selected angles, for faster acquisition.
• Time estimation values are more accurate and are updated throughout the automated acquisition.
• Various other usability and performance improvements.

Tomography software

Description of updates

• Sample navigation, batch mode and dose symmetric tilt scheme are now available in STEM mode. Tomography 4 Software is no longer required.
• Set up of EDS acquisition (using Thermo Scientific Velox Software) has been improved.
• Defining optics and detector settings for STEM has been simplified.
• Search maps can be acquired faster when using image/beam shift (beta). Non-square maps are now supported.
• Column valves open semi-automatically when needed.
• As opposed to EPU, the column valves are not opened automatically to avoid sample damage.
• An estimation of the acquisition time is available before starting an automated acquisition.
• On Talos systems, it is now possible to visualize the beam diameter for more accurate batch position setup.
• Various other usability and performance improvements.

Tomography software

Description of updates

• Search maps are now available to acquire and use medium magnification maps to improve navigation on your sample and more accurately add acquisition areas.
• All sample navigation features that are available in batch mode can also be used for single tilt series.
• Holder calibrations and predictions can be used for the dose-symmetric tilt scheme.
• Holder calibrations are saved for specific holder types and predictions automatically use the correct type.
• Auto-eucentric by stage tilt now accepts a maximum acceptable z-height deviation.
• Different multiple defocus values can be set for consecutive batch positions automatically.
• In "Batch" mode, you can select a subset of position for acquisition.
• During automated batch acquisition, you can skip the current position in case of problems.
• Various other usability and performance improvements.

TOMO acquisition software

Applicable instruments

• Krios Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
  
• Talos F200C
• Talos L120C

Description of updates

• Movie Player is available to easily review acquired data. When in batch mode, the positions are conveniently listed to quickly select different positions.
• Tilt series results can be exported as movies in standard H.264 format.
• Improved annotations in Atlas and Overview image scale based on zoom level, and only show detailed information such as beam diameter when appropriate. If positions are too close, they are grouped together.
• Improved annotations in Search image show not just the annotations for the position to be added, but also for all other previously added positions close by. They also allow you to move Focus and Tracking areas at the same time, instead of separately as before.
• Holder calibration results can be opened and viewed within the app.
• Scaling of non-square images is improved when resizing the app.
• Handling of missing or corrupt presets has improved.
• Various other usability and performance improvements were made.

Availability

Free of charge for service contracts

TOMO acquisition software

Applicable instruments

• Krios Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
  
• Talos F200C
• Talos L120C

Description of updates

• Improved annotations in the Overview image show details of all positions, including the focus and tracking areas.
• Multiple Overview images can be saved to easily navigate across different grid squares.
• Acquire a Single Atlas on autoloader systems even when the autoloader status is not initialized (e.g. no cassette docked).
• Metadata are saved in MDOC format.

Availability

Included in service contracts

TOMO acquisition software

Applicable instruments

• Krios Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
  
• Talos F200C
• Talos L120C

Description of updates

• Tomography > Template Definition and Batch Positions:
  • The Condition Area with Stage function is now available.
• Tomography > Batch Positions:
  • The Acquire Overview function acquires and displays an image of the Grid Square in which the Batch Positions are identified with labeled markers. The color of each marker corresponds with the status of the Batch Position. The Overview image makes it easier to navigate and to identify the locations for new and existing Batch Positions.

Availability

For first-time installations, a 90-day Trial License is available to evaluate the software

TOMO acquisition software

Applicable instruments

• Krios G3i Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
  
• Talos F200C
• Talos L120C

Description of updates

• Tomography > Session Setup:
  • For the Gatan K3 camera, the following output formats are available for dose fraction images:
    • Gain-normalized MRC images.
    • Non-gain normalized LZW-compressed TIFF images. For non-gain normalized images, a gain reference image will be saved as well.
  • After a single or batch tilt series ends, an e-mail can be sent to a list of e-mail addresses. The e-mail contains limited status information about the automated acquisition.
• Tomography > Batch Positions:
  • If an Atlas image is available for the currently loaded specimen, then this Atlas image can be used to:
    • Navigate to different locations on the specimen.
    • Display the location and status of batch positions.
  • It is possible to add batch positions with different start angles.

Availability

Free of charge for service contracts

TOMO acquisition software

Applicable instruments

• Krios G3i Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
  
• Talos F200C
• Talos L120C

Description of updates

Tomography > Automated Acquisition:

• The Switch Angle functionality is no longer disabled.
  • For the Gatan K3 camera, the Automated Acquisition procedure acquires a fresh Dark Reference at the start of each Tilt Series.
  • On Talos L120 systems, the Thermionic Filament can now be switched off at the end of a run.

Availability

No license is required to upgrade from Tomo 4.x to 5.x

TOMO acquisition software

Applicable instruments

• Krios G3i Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
  
• Talos F200C TEM
• Talos L120C TEM

Description of updates

• New user interface:
  • The TEM Tomography application now features the same look & feel and the other TEM / cryo-EM applications: EPU and EPU-D
• The Optimized Position calibration is re-introduce
• The Holder Prediction calibration is re-introduced
• Tomo, R4.14 is required for STEM. (installed automatically)

Availability

No license update is required to upgrade from Tomo 4.x to 5.x

TOMO acquisition software

Applicable instruments

• Krios G3i Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
  
• Talos F200C TEM
• Talos L120C TEM

Description of updates

• New user interface:
  • The TEM Tomography application now features the same look & feel and the other TEM / CryoEM applications: EPU and EPU-D.
  • The setup of the following functionalities has been redesigned for improved ease-of-use:
    • Batch Positions
    • Tilt Series
    • Image Filter settings
  • Tomography > Data Acquisition The Dose Symmetric Tilt Scheme schedules the tilt angle sequence so that the accumulated dose at low tilt angles is minimized. On dose-sensitive specimens, the Dose Symmetric Tilt Scheme provides the highest quality images for 3D reconstruction.
  • Preparation > Acquisition and Optics Presets The Gatan Quantum 1967 (with K3 camera) is now supported.
• Improvements:
  • New acquisition engine The new Tomography acquisition engine provides faster and more robust automated acquisition.

Availability

Free of charge for service contracts

STEM and TEM software supporting imaging and analysis

Description of updates

• Special Marker for Central Beam in Diffraction Patterns: We have added a special marker to mark the position of the central beam in diffraction patterns. This tool helps users perform accurate tilting with the click-tilt feature (introduced in version 3.12). Now, it is no longer necessary to center the diffraction pattern on the display to perform accurate click-tilt. Users can mark the position of the central beam with the new marker and click-tilt towards the marked center every time.
  
  
• Improved Usability of SmartCam: Previously, we enabled different detector overlays on SmartCam, like the Flucam viewer. However, since not all detectors are available in different modes, Velox now only shows overlays that are operational in the active mode. For example, STEM detector overlays will be hidden in TEM mode.
  
  
• “Blank Beam When Idle”: The “Blank beam when idle” preset on the Ceta camera now also works in conjunction with SmartCam. When the “blank beam when idle” checkbox is active, the beam will automatically be blanked when SmartCam is idle. This safeguard ensures that the sample remains protected during periods of inactivity, reducing the risk of accidental damage.
  
  
• Enhanced Button Styling: We have enhanced the button styling for improved experience and visibility. Buttons now transition from a subtle appearance to a clearly visible one when clicked or in use. This enhancement aims to clearly identify the camera in use and provide a clearer understanding of other ongoing actions, thereby minimizing confusion and potential errors. With unified styling, we hope to improve user confidence and satisfaction in camera usage.

Compatibility: Titan SW 3.16.x – 3.21.x / Talos SW: 2.16.x – 2.21.x.

For more details please visit here.

STEM and TEM software supporting imaging and analysis

Description of updates

• On-display text for SmartCam: This feature provides users with information regarding the reasons for the absence of an image, enabling quick identification the microscope status.
• Improved display layout: The Layout toolbar now adapts its options based on the number and type of displays opened.
• Synchronized image rotation: The stage movements with joystick are now synchronized with Image rotation of SmartCam, similar to how image rotation works with Ceta camera.
• Overexposed areas indication on Ceta display: Overexposed areas are now clearly indicated on the Ceta display, providing users with the ability to make informed adjustments. The indication aligns with the histogram range, ensuring accurate representation of image exposure levels.
• Generic improvements: these include customizable precision for annotation tools, a new data bar item combining microscope mode and magnification/camera length information, support for custom readout areas in 4D-STEM experiments with virtual detectors, and enhanced error messages during sample loading for improved clarity.
• SmartCam now is integrated into Velox. It includes navigation and tilting with mouse clicks, improved display switching, image rotation, detector overlays and more.
  SmartCam requires TEM SW version (TEM server) 2.17.1 for Talos and 3.17.1 for Themis/Spectra. For optimal performance, ensure that all necessary system calibrations, including diffraction calibration and camera-to-camera calibration, have been performed.

Compatibility: Titan SW 3.15.x – 3.20.x / Talos SW: 2.15.x – 2.20.x.

For more details please visit here

STEM and TEM software supporting imaging and analysis

Description of updates

• SmartCam Integration: SmartCam now integrated in Velox and supports click-to-move navigation and click-tilt functions, allowing users to move the stage to a location with a simple double-click on the image or diffraction. Experience this feature in action here.
• File Format Update for EDS SI Data: Velox EDS SI data files created in version 3.11 or earlier will be automatically converted to the current format when opened with Velox version 3.12 or later, with a backup file created for data safety. Please note, files created with Velox 3.12 or later will not be compatible with earlier Velox versions (3.11 or before). This change will not impact the integrity of the data.
• SmartCam requires TEM SW version (TEM server) 2.17.1 for Talos and 3.17.1 for Themis/Spectra. For optimal performance, ensure that all necessary system calibrations, including diffraction calibration and camera-to-camera calibration, have been performed.

Compatibility: Titan SW 3.14.x – 3.19.x / Talos SW: 2.14.x – 2.19.x.

For more details please visit here

STEM and TEM software supporting imaging and analysis

Description of updates

• Multi-selection feature for annotations 
• Introduction of a Digital Micrograph plugin for loading images from an EMD file
• Support for Falcon C Detector has been implemented

Compatibility: Titan SW 3.14.x – 3.19.x / Talos SW: 2.14.x – 2.19.x.

For more details please visit here

STEM and TEM software supporting imaging and analysis

Description of updates

• Pause and End Session. 
• License Management.

Compatibility: Titan Cryo-TEM SW 3.12.x – 3.17.x / Talos TEM SW: 2.12.x – 2.17.x.

For more details please visit here

STEM and TEM software supporting imaging and analysis

Description of updates

• OptiSTEM/AutoSTEM directly accessed via Velox Software (requires latest TEM server)
• Improvements for 4D STEM: virtual STEM images for the live preview during acquisition (requires latest TEM server)
• Radial intensity profile:
  • Manual controls
  • Automatic centering on diffraction pattern
  • Save/load
• Spectrum image data export to lispix format
• Ability to park beam in STEM mode outside of the field-of-view

For more information please visit the Velox Software  page

STEM and TEM software supporting imaging and analysis

Description of updates

• EDS Batch Processing (New paid option. If interested, please contact your account manager for more information).
  • Process multiple Spectrum Images from different Velox files
  • Apply quantification settings from the selected experiment
  • Store re-quantified datasets
  • Optionally export the elemental maps and up to five Color Mix combinations
  • Supports Velox .emd files recorded by Velox and Metrios SW
• Improvements for Electron Dose Control (EDC)
  The dose can now be set and edited from the Velox Acquisition settings panel. It will change the beam current to achieve the desired dose. Moving the mouse over a STEM image in Velox will display the Dose Per Pixel (requires Panther STEM detector-

• Radial intensity profile
• EDS fits improvements for Yb

STEM and TEM software supporting imaging and analysis

Description of updates

• Electron Dose Control for Spectra XCFEG (this is new option, please read details in the release notes and contact your account manager if you are interested)
• Key modifier is added to draw multiple shapes without need to reselect
• Custom start number for the file name
• Absorption correction enabled for Bruker 30mm2 detector
• Number of stability and performance improvements

To obtain update:

STEM and TEM software supporting imaging and analysis

Description of updates

• Drift compensated multi-frame acquisition is available for EDS+EELS
• EDS improvements: Msa file format spectrum load is now supported. Warning for the size of Spectrum image. Improved loading of large prefiltered Spectrum images. The performance of loading files greater than 8GB with prefiltered Spectrum images has been improved by up to 60%.
• Annotations supported in file menu export.
• Keyboard shortcut for cross-hair is added.
• Experiment files can be saved in sequential file numbering.
• Spectrum plot axis boundaries can now be set through the object properties panel.

To obtain update: 

STEM and TEM software supporting imaging and analysis

Description of updates

• Image rotation for TEM images in post processing.
• Keyboard shortcuts for acquisition.
• Persisting pre-filter selection with switch of quantification modes.
• Option to save data in ASCII format for compatibility with old scripts.
• EER support for Falcon 4 cameras.
• Small improvements for export, including automatically adjusted pixel size for resampled 8bit tiffs and selection persistence.

STEM and TEM software supporting imaging and analysis

Description of updates

• Sequential numbering and Sample/User fields for databar 
• Performance improvements For more information and installer please go to:

Software (codecs) for viewing acquired images (via Windows explorer)

Applicable instruments

• Krios G3i Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
• Talos F200C TEM
• Talos L120C TEM

Description of updates

• Added support for MRC Mode 12 files
• Added support for MRC stacks with more than 65535 frames
• Improved contrast and brightness for electron counted images

Tomography post-alignment and reconstruction module

Description of updates

• Rename "Reduce" tab to "Pre-processing Data" tab.
  
• Inspect3D now integrates Motion Correction support on the "Pre-processing Data" tab.
  
• Reconstruction preview follows the selected parameters.
• Problem with odd size images in StackAlignment tab is fixed.
• IMOD files can now be imported to Inspect 3D.
• Support for Serial EM MRC-2014 variant.
• EDS reconstructions: ability to apply alignment to “sparse” tilt series.
• Tilt axis adjustment parameters are now saved in the shift file.
• 30 day trial license support.
• Some small fixes and improvements. 

Availability

Free of charge for service contracts

Note: Inspect 3D should not be installed on Microscope PC.

Single Particle Analysis (SPA) workflow guidance (iOS, Android)

Applicable instruments

• Krios G3i Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica S/TEM
• Talos F200C S/TEM

Description of updates

• Project name is no longer mandatory
• Hide Workflow Assistant if empty
• Now support two images per step
• Added info on how to obtain a full license (login screen)
• Improved workflow text formatting

Availability

• Free of charge (via lite version on login screen)
• Full version available via Accelerate & Advance service packages

Software (codecs) for viewing acquired images (via Windows explorer)

Applicable instruments

• Krios G3i Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
• Talos F200C TEM
• Talos L120C TEM

Description of updates

• Velox EMD files will not be associated with the Windows Photo Viewer anymore when Velox is installed
• The Imaging Codec Pack installer is now signed with the FEI certificate

Software (codecs) for viewing acquired images (via Windows explorer)

Applicable instruments

• Krios G3i Cryo-TEM
• Glacios Cryo-TEM
• Talos Arctica TEM
• Talos F200C TEM
• Talos L120C TEM

Description of updates

• Improved Windows 10 stability

Availability

Free of charge for service contracts