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