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Releases: NIEHS/SmartScope

v0.9.1

11 Jul 01:46
@JoQCcoz JoQCcoz
0.9.1
f9b90d4
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v0.9.1

Main Changes

  • Reworked the statistics tab to give more information such as a CTFfit plot, remaining time, number of total holes remaning and total time spent.
  • Added AFIS capability that makes use of the coma vs Image-Shift SerialEM calibration.
  • Added auto Hardware dark timer in the collection parameters
  • Complete rework of the preprocessing pipeline API to allow building other pipelines in the near future (i.e. Scipion, Relion, Cryosparc Live, etc.)

Bug fixes

  • Ptolemy hole finder is now more robust with fallback in unlikely case of failure. (Usually very close to grid bars)
  • Fixed issue with the setup form in newer versions of chrome.

What's Changed

Full Changelog: 0.9...0.9.1

Contributors

JoQCcoz
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v0.9

11 Apr 00:15
@JoQCcoz JoQCcoz
0.9
bdcef96
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v0.9

Main changes

Added multi-shot per hole for high-throughput data collection
Added automatic positioning of the autofocus position on holey grids

Other Improvements

Ability to change protocol from web interface
Ability to view the state of the microscopes and their current sessions.
Added support for SerialEM 4.1
Added saving frames with fake scope mode
Added additional filters to high_magnification endpoints.

Minor changes

Significantly reduce the repository size by removing the static files from bootstrap
Added htmx support to reduce the amount of javascript code
Changed the frontend css framework to the latest version of bootstrap (5.2)

What's Changed

Full Changelog: 0.8...0.9

Contributors

JoQCcoz
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v0.9 release candidate 1

14 Mar 00:23
@JoQCcoz JoQCcoz
0.9-rc.1
51e7c2d
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v0.9 release candidate 1 Pre-release
Pre-release

Main changes

  • Added multi-shot per hole for high-throughput data collection
  • Added automatic positioning of the autofocus position on holey grids

Other Improvements

  • Ability to change protocol from web interface
  • Ability to view the state of the microscopes and their current sessions.
  • Added support for SerialEM 4.1

Minor changes

  • Significantly reduce the repository size by removing the static files from bootstrap
  • Added htmx support to reduce the amount of javascript code
  • Changed the frontend css framework to the latest version of bootstrap (5.2)

Pull requests

Full Changelog: 0.8...0.9-rc.1

Contributors

JoQCcoz
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v0.8

14 Feb 04:23
@JoQCcoz JoQCcoz
0.8
000050f
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v0.8

Main changes

  • Simplified installation procedure
    • Added a docker repository with prebuilt images
    • Abstracted the docker commands behind a simple bash script
  • Grid metadata can now be exported and re-imported into the same or new SmartScope instance.
    • This feature will require more work for automatically creating the directory structure and move the data automatically but this is a start.
  • Added a :doc:/protocolAPI/index to add more flexibility to the workflow.
  • Ptolemy is now integrated as an :doc:external plugin</external_plugins/index>.
    • Used as a medium mag hole finder for refinining the hole positions. Targeting of the holes is now much more precise.
  • Support for Falcon detectors
    • Created an interface without the gatan-only serialem commands
    • V0.8b2 has a consolidated interface for gatan and Falcon
  • Added CTFFit display on the square maps
  • Added a square recentering procedure to the square acquisition routine and changed the eucentricity back to the default sem.Eucenticity(1) command instead of the custom one in Search.
  • Added a default_collection_params.yaml under config/smartscope to easily modify the default values and disable fields in the Run Smartscope page for the collection parameters section.
  • Extended the API query by adding a /detailed sub-route to the /api/squares and /api/holes route. Can be used both single or multiple objects query.
  • Added download buttons for the Atlas and Square maps to easily download the raw, mrc and png files from the web interface
  • Added scale bars and extra metadata to the High-mag cards
  • Added image-shift offsets for the hole imaging to get a sampling of the ice across the hole.
    • Can also set a hard offset value to acquire all targets with specific offset.
  • Changed the plugin interface to make it more usable and flexible.

Minor changes

  • Added notification for commands that are currently issued to the backend and waiting for response.
  • Added a link to submit issues on gihub in the navbar
  • Now using an updated version of the SerialEM python module to access new commands
  • Frames default name is now automatically set to date_gridname_???.tif
  • The display options are now preserved if the webpage is refreshed instead of resetting to default.
  • Added more default environment variables to the Dockerfile to simplify the docker-compose.yml file.
  • Can now click on the hole to view medium mag before all the high mag images are acquired

Bug fixes

  • Fixed not being able to click on the edge of maps on smaller browser windows
  • Fixed issue with the Regular Pattern plugin not setting targets on the entire width of the K3 images
  • Fixed issues with the Regrouping BIS command not putting all the targets correctly back into the queue
  • Moved all the database writing actions back to restAPI for authentication simplicity. More secure until authentication can be confirmed in the websocket layer.
    • Websocket still used for receiving data from the backend
  • Mouse cursor properly changing when hovering over the sidepanel links
  • Fixed issue where toggling the legend display on a map didn't remove the scale bar, thus preventing clicking the areas beneath it.
  • Fixed issue with column valves not closing after session.
  • Fixed issue with being unable to click sqaures on the right part of the atlas while using a small browser window.
  • Added atlas and medium mag completion times
  • Fixed where the active square would not turn yellow until eucentricity was finished
  • Fixed where data could be fetched by all logged-in users to any groups through the REST api. Now gives permission denied if the user isn't staff or in the group.
  • Fixed where Regrouping the BIS grouping from the webUI was not working.
  • Fixed few bugs with the preprocessing pipeline crashing
  • Fixed error with protocol selection when Lacey carbon and negative stain grids are selected.
  • Fixed issue with django-filters not being active when querying the REST API.
  • Fixed issue with the Dockerfile where pip was not found during build.
  • Found a very old issues with the build montage and the piece centers were not correctly calculated
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v0.8 release candidate 2

07 Feb 15:36
@JoQCcoz JoQCcoz
0.8-rc.2
6c0c5ce
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v0.8 release candidate 2 Pre-release
Pre-release

Main changes

Simplified installation procedure and updated repo Readme.

Bug fixes

Full Changelog: 0.8-rc.1...0.8-rc.2

Contributors

JoQCcoz
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v0.8 release candidate 1

13 Jan 20:40
@JoQCcoz JoQCcoz
0.8-rc.1
611da55
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v0.8 release candidate 1 Pre-release
Pre-release

Main changes

  • Grid metadata can now be exported and re-imported into the same or new SmartScope instance.
    • This feature will require more work for automatically creating the directory structure and move the data automatically but this is a start.
  • Added a :doc:/protocolAPI/index to add more flexibility to the workflow.
  • Ptolemy is now integrated as an :doc:external plugin</external_plugins/index>.
    • Used as a medium mag hole finder for refinining the hole positions. Targeting of the holes is now much more precise.
  • Support for Falcon detectors
    • Created an interface without the gatan-only serialem commands
    • V0.8b2 has a consolidated interface for gatan and Falcon
  • Added CTFFit display on the square maps
  • Added a square recentering procedure to the square acquisition routine and changed the eucentricity back to the default sem.Eucenticity(1) command instead of the custom one in Search.
  • Added a default_collection_params.yaml under config/smartscope to easily modify the default values and disable fields in the Run Smartscope page for the collection parameters section.
  • Extended the API query by adding a /detailed sub-route to the /api/squares and /api/holes route. Can be used both single or multiple objects query.
  • Added download buttons for the Atlas and Square maps to easily download the raw, mrc and png files from the web interface
  • Added scale bars and extra metadata to the High-mag cards
  • Added image-shift offsets for the hole imaging to get a sampling of the ice across the hole.
    • Can also set a hard offset value to acquire all targets with specific offset.
  • Changed the plugin interface to make it more usable and flexible.

Minor changes

  • Added a link to submit issues on gihub in the navbar
  • Now using an updated version of the SerialEM python module to access new commands
  • Frames default name is now automatically set to date_gridname_???.tif
  • The display options are now preserved if the webpage is refreshed instead of resetting to default.
  • Added more default environment variables to the Dockerfile to simplify the docker-compose.yml file.
  • Can now click on the hole to view medium mag before all the high mag images are acquired

Bug fixes

  • Moved all the database writing actions back to restAPI for authentication simplicity. More secure until authentication can be confirmed in the websocket layer.
    • Websocket still used for receiving data from the backend
  • Mouse cursor properly changing when hovering over the sidepanel links
  • Fixed issue where toggling the legend display on a map didn't remove the scale bar, thus preventing clicking the areas beneath it.
  • Fixed issue with column valves not closing after session.
  • Fixed issue with being unable to click sqaures on the right part of the atlas while using a small browser window.
  • Added atlas and medium mag completion times
  • Fixed where the active square would not turn yellow until eucentricity was finished
  • Fixed where data could be fetched by all logged-in users to any groups through the REST api. Now gives permission denied if the user isn't staff or in the group.
  • Fixed where Regrouping the BIS grouping from the webUI was not working.
  • Fixed few bugs with the preprocessing pipeline crashing
  • Fixed error with protocol selection when Lacey carbon and negative stain grids are selected.
  • Fixed issue with django-filters not being active when querying the REST API.
  • Fixed issue with the Dockerfile where pip was not found during build.
  • Found a very old issues with the build montage and the piece centers were not correctly calculated
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v0.7

02 Aug 22:40
@JoQCcoz JoQCcoz
v0.7
9e58e2a
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v0.7

Added random offset for high-mag acquisition so sample ice across the hole.
Revamped Preprocessing pipeline including new abstract class for easier worflow integration.

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