EM-Software-Updates

Stay ahead with the latest electron microscopy software updates

We are always looking to improve your electron microscopy experience, whether through enhanced access to service experts, easy to use step-by-step guides, or hands-on training. We also know your electron microscopy lab requires maintenance to stay in top shape. A critical component of this ecosystem is powerful software that enables you to get the best results possible from your instrumentation. That is why we offer a constant stream of improvements and updates to our software, ensuring you are able to achieve your goals as quickly and easily as possible.

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Release Notes
EPU

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

To obtain update, download here.

SPA aquisition software

Applicable instruments

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).

To obtain update, download here.

SPA aquisition software

Applicable instruments

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.

To obtain update, download here.

SPA acquisition software

Applicable instruments

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

To obtain update, download here.

SPA acquisition software

Applicable instruments

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 > Acquision and Optics Presets: The most recent acquired preview for each Present remains availabe until a new Preview is acquired. On the preview image, the context menu provides navigation options.
  • Preparations > Acquision 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.

To obtain update, download here.

SPA acquisition software

Applicable instruments

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.

To obtain update: Download here

EPU-D

SPA acquisition software

Description of updates

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

To obtain update, download here.

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

Applicable instruments

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.

To obtain update, download here.

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

Applicable instruments

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.

To obtain update, download here.

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

Applicable instruments

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

Contact our on-site software service for update.

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

Applicable instruments

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.

Contact our on-site software service for update.

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

Applicable instruments

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

Contact our on-site software service for update.

TEM server

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

Contact our on-site software service for update.

Server software for life sciences

Applicable instruments

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

Contact our on-site software service for update.

Server software for life sciences

Applicable instruments

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

Contact our on-site software service for update.

Server software for life sciences

Applicable instruments

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:

Contact our on-site software service for update.

Server software for life sciences applications

Applicable instruments

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

Contact our on-site software service for update.

Server software for life sciences applications

Applicable instruments

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

Contact our on-site software service for update.

Server software for life sciences

Applicable instruments

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

Contact our on-site software service for update.

Server software for life sciences

Applicable instruments

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

Contact our on-site software service for update.

Server software for life sciences

Applicable instruments

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:

Contact our on-site software service for update.

Server software for life sciences applications

Applicable instruments

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

Contact our on-site software service for update.

Server software for life sciences applications

Applicable instruments

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

Contact our on-site software service for update.

Tomography

TOMO acquisition software

Applicable instruments

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

Contact our on-site software service for update.

TOMO acquisition software

Applicable instruments

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

Contact our on-site software service for update.

TOMO acquisition software

Applicable instruments

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

Contact our on-site software service for update.

TOMO acquisition software

Applicable instruments

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

Contact our on-site software service for update.

Other

Electron Microscope data management

Applicable instruments

Description of updates

  • New Features: Basic export functionality
    • Manual, batch Export
    • Export on type (Raw, Processed)
    • Export Job Monitoring
    • Disk Cleanup
    • File support
      • EER, Dark & Gain file support
      • Dataset Manual Archiving improvements
    • New EQM features: Output for D2i
  • Improvements
    • Improve Entity PostgreSQL databases charts management
    • Core Library exceptions management
    • Get project Action list
  • Bug Fixes
    • Deleted datasets still visible
    • Swagger documentation doesn’t work for some services
    • Metadata deletion message does not display the targeted metadata name
    • Permission deletion message states that a “user” will be deleted
    • Cannot retry a failed upload
    • Metadata service times out when re-indexing a large amount of data

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

Applicable instruments

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

To obtain update: Download here

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

Applicable instruments

Description of updates

  • Improved Windows 10 stability

Availability

Free of charge for service contracts

To obtain update: Download here

Tomography post-alignment and reconstruction module

Applicable instruments

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

Contact our on-site software service for update.

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

Applicable instruments

Description of updates

  • Amira-Avizo2D support

Contact our on-site software service for update.

 
 

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

Applicable instruments

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

To obtain update, download here: