0.9.4-rc.1

Main Changes

• CryoARM microscope are now fully supported.
• Complete rework of the aperture control. Apertures can now be specified in the collection parameters form.
• Added a automated beam re-centering routine.
• Changes the image coordinates to stage conversion to use the SerialEM BufImageToStageMatrix instead of the pixel size and rotation angle from the mdoc file. This will allow to use the high-defocus calibration and other image-shifts to convert coordinates more precisely.

Minor Changes

• Added FORCE_MDOC_TARGETING environment variable to disable the new coordinate conversion and use the original mdoc values.
• Added SKIP_WEBSOCKET_DURING_DATACOLLECTION environment variable to diable websockets during data collection to enhance stability during long sessions. This is a temporary fix until the websockets are reworked.
• Greatly increased the speed of multishot per hole pattern calculations.
• Fixed some issues with square and hole selection selecting targets outside of the allowed classes.

Complete list of commits

• created models and initial migrations by @JoQCcoz in #293
• Adding tags by @JoQCcoz in #294
• adding restore state by @JoQCcoz in #295
• adding remove condenser for square images jeol by @JoQCcoz in #296
• added more podman support to smartscope.sh by @JoQCcoz in #298
• Change to aperture controls by @JoQCcoz in #299
• Adding tags by @JoQCcoz in #300
• edit apertureState by @JoQCcoz in #301
• fixing apertureState by @JoQCcoz in #302
• change jeolinterface by @JoQCcoz in #303
• change serialeminterface by @JoQCcoz in #304
• remove stupid log by @JoQCcoz in #305
• add searhc before atlas jeol and logging bug by @JoQCcoz in #306
• remove log by @JoQCcoz in #308
• checking istostagematrix by @JoQCcoz in #309
• adding logging by @JoQCcoz in #310
• adding test command for coordinate conversion by @JoQCcoz in #311
• adding coordinates test commands by @JoQCcoz in #312
• Fix issues with target selection and grouping by @JoQCcoz in #313
• made z-move optional when moving stage. by @JoQCcoz in #314
• Adding tags by @JoQCcoz in #315
• Rework the selectors by @JoQCcoz in #316
• debug jeol by @JoQCcoz in #317
• fix wrong axis lenght used for y-flip by @JoQCcoz in #318
• Dev by @JoQCcoz in #319
• fix issues with atlas by @JoQCcoz in #320
• Fix the atlas command for the JEOL by @JoQCcoz in #321
• Bug fixes by @JoQCcoz in #322
• added inventory command on jeol scopes by @JoQCcoz in #323
• change loadcartridge by @JoQCcoz in #324
• edit jeolserialeminterface by @JoQCcoz in #325
• flip isx by @JoQCcoz in #326
• flip isx by @JoQCcoz in #327
• Change to the multishot per hole calculator by @JoQCcoz in #328
• added environment variable to force_mdoc_targeting by @JoQCcoz in #329
• fix synthax error by @JoQCcoz in #330
• Added ability to disable vector-based target coordinates by @JoQCcoz in #331
• few fixes and addition for JEOL by @JoQCcoz in #332
• added buffer to atlas vectors by @JoQCcoz in #333
• fix binning issues with montages by @JoQCcoz in #334
• fixing binning atlas by @JoQCcoz in #335
• Adding tags by @JoQCcoz in #336
• added loggin to beam recentering by @JoQCcoz in #337
• Ability to turn off websockets during data collection to prevent cach… by @JoQCcoz in #338
• Dev by @JoQCcoz in #339

Full Changelog: 0.9.3.1...0.9.4-rc.1

0.9.3.1

What's Changed

• Fixed bug with aperture controls in TFS microscopes.
• Fixed bug with creating the frames directory for EER files.
• The Window Frames Directory should now be left empty for Falcon Detectors. Help text changed to reflect this behavior.

Full Changelog: 0.9.3...0.9.3.1

0.9.3

What's Changed

• merge 0.9.2 to dev by @JoQCcoz in #244
• New selectors by @JoQCcoz in #246
• tested new frames directories and preprocessing by @JoQCcoz in #247
• New selectors by @JoQCcoz in #248
• fix preprocessing pipeline by @JoQCcoz in #249
• change ctffind params by @JoQCcoz in #251
• added lattice extension by @JoQCcoz in #253
• New selectors by @JoQCcoz in #254
• New selectors by @JoQCcoz in #255
• New selectors by @JoQCcoz in #256
• Behavior of the selector completed by @JoQCcoz in #257
• added save to session and tooltips by @JoQCcoz in #258
• New selectors by @JoQCcoz in #259
• added grid_wide regroup bis to webUI by @JoQCcoz in #260
• New selectors by @JoQCcoz in #261
• version bump by @JoQCcoz in #262
• Dev by @JoQCcoz in #263
• New selectors by @JoQCcoz in #264
• New selectors by @JoQCcoz in #265
• fix error in export_grid command by @JoQCcoz in #266
• fixed import issue with import-export workflow by @JoQCcoz in #267
• New selectors by @JoQCcoz in #268
• removed repetitive debug message by @JoQCcoz in #269
• Stable by @JoQCcoz in #270
• Protocol rework by @JoQCcoz in #271
• Protocol rework by @JoQCcoz in #272
• Protocol rework by @JoQCcoz in #273
• fix typo by @JoQCcoz in #274
• fix earlyreturn on falcon4 by @JoQCcoz in #275
• added delay before grabbing buffer by @JoQCcoz in #276
• change default focusafterdistance value by @JoQCcoz in #277
• remove symlink from preprocessing by @JoQCcoz in #278
• fix process_from_avg by @JoQCcoz in #279
• removing symlink by @JoQCcoz in #280
• Dev by @JoQCcoz in #281
• added going to highmag before LD in jeol and save transform matrix by @JoQCcoz in #282
• fix bugs by @JoQCcoz in #283
• fix bugs by @JoQCcoz in #284
• fix issue with mousedown conversion by @JoQCcoz in #285
• fix issues with preprocessing by @JoQCcoz in #286
• Stable by @JoQCcoz in #287
• fix error in report_mag for JEOL scopes by @JoQCcoz in #288
• Stable by @JoQCcoz in #289

Full Changelog: 0.9.2.3...0.9.3

0.9.3-rc.3

What's Changed

• New selectors by @JoQCcoz in #264
• New selectors by @JoQCcoz in #265
• fix error in export_grid command by @JoQCcoz in #266

Full Changelog: 0.9.3-rc.1...0.9.3-rc.3

0.9.3-rc.1

Main Changes

• Added new menu to interact with the selectors on the grid. You may now bulk-select holes on the entire grid based on their gray-level intensity.
• Lattice extention. It is now possible to extend the hole lattice on the grid to pick the holes that were missed by the hole finder.
• New global commands. Regroup BIS on the entire grid instead of single square
• Completely reworked the target selection process. Should now be more reliable

What's Changed

• New selectors by @JoQCcoz in #246
• tested new frames directories and preprocessing by @JoQCcoz in #247
• New selectors by @JoQCcoz in #248
• fix preprocessing pipeline by @JoQCcoz in #249
• change ctffind params by @JoQCcoz in #251
• added lattice extension by @JoQCcoz in #253
• New selectors by @JoQCcoz in #254
• New selectors by @JoQCcoz in #255
• New selectors by @JoQCcoz in #256
• Behavior of the selector completed by @JoQCcoz in #257
• added save to session and tooltips by @JoQCcoz in #258
• New selectors by @JoQCcoz in #259
• added grid_wide regroup bis to webUI by @JoQCcoz in #260
• New selectors by @JoQCcoz in #261
• version bump by @JoQCcoz in #262

Full Changelog: 0.9.2.3...0.9.3-rc.1

v0.9.2.3

• Updated square finder for better perfomance on full grid atlases
• Extented JEOL Cryo ARM support
• Fixed error where no targets are found on square crashes run.
• Fixed issue with manual target addition not working
• Added import-export commands to transfer sessions between instances.

What's Changed

• merge stable into latest by @JoQCcoz in #245

Full Changelog: 0.9.2...0.9.2.3

v0.9.2

Main changes

• Added aperture controls for TFS microscopes
• Added Gridswapper for JEOL cryoARM microscope
• Added ability to automatically flash the cold FEG every X hours.
• Added REST API endpoints to upload highmag images and power spectrum and fetch detailed information about holes.
• Added button to interrupt/skip started targets.
• Added stage limits where all targets beyond 990um from the stage origin won't be selected and can't be selected.
• Added X,Y offsets behavior to realign the atlas and the square magnification. Similar to Shift To Marker in SerialEM.
• Added a command to calculate and optionally the X,Y offset for a specific detector based on the history of square recentering.
• Start of a big backend refactoring.
• New management commands for database backups.
• Added ways to customize save locations based on users and/or groups.

What's Changed

• Cli plot by @JoQCcoz in #197
• build development environment by @tiezheng-yuan-nih in #199
• default value of display_type by @tiezheng-yuan-nih in #200
• Cleaning up dev environment by @JoQCcoz in #203
• Svgrendering by @JoQCcoz in #206
• fixed read_config by @JoQCcoz in #207
• Dev by @JoQCcoz in #208
• fixed position of numbers in svg by @JoQCcoz in #209
• set environments with response to updates of Jo's dev branch by @tiezheng-yuan-nih in #210
• process higmag by @tiezheng-yuan-nih in #211
• example of unit testing by @tiezheng-yuan-nih in #216
• decouple autoscreen by @tiezheng-yuan-nih in #217
• Scopeinterface by @JoQCcoz in #218
• more debugging by @JoQCcoz in #219
• 0.9.2 rc.1 by @JoQCcoz in #220
• fixed ctf image not loading by @JoQCcoz in #221
• 0.9.2 rc.1 by @JoQCcoz in #222
• 0.9.2 rc.1 by @JoQCcoz in #223
• Stable by @JoQCcoz in #226
• Initial framework for CryoSPARC Live integration by @ccgauvin94 in #225
• Stable by @JoQCcoz in #227
• added download_testfiles command by @JoQCcoz in #228
• Add atlas_offset to the square acquisition by @JoQCcoz in #229
• Added ability to skip started targets. by @JoQCcoz in #230
• Stable by @JoQCcoz in #231
• Added stage limits by @JoQCcoz in #232
• updated tooltips by @JoQCcoz in #233
• CryoSPARC Live Connection by @ccgauvin94 in #234
• added logging to aperture exchange by @JoQCcoz in #237
• Custom paths by @JoQCcoz in #238
• Dev by @JoQCcoz in #239
• added db management commands by @JoQCcoz in #240
• Dev by @JoQCcoz in #241
• added alternate login logic by @JoQCcoz in #242
• 0.9.2 by @JoQCcoz in #243

New Contributors

• @tiezheng-yuan-nih made their first contribution in #199
• @ccgauvin94 made their first contribution in #225

Full Changelog: 0.9.1...0.9.2

v0.9.2-rc.4

Main changes

• Added aperture controls for TFS microscopes
• Added Gridswapper for JEOL cryoARM microscope
• Added ability to automatically flash the cold FEG every X hours.
• Added REST API endpoints to upload highmag images and power spectrum and fetch detailed information about holes.
• Added button to interrupt/skip started targets.
• Added stage limits where all targets beyond 990um from the stage origin won't be selected and can't be selected.
• Added X,Y offsets behavior to realign the atlas and the square magnification. Similar to Shift To Marker in SerialEM.
• Added a command to calculate and optionally the X,Y offset for a specific detector based on the history of square recentering.
• Start of a big backend refactoring.

What's Changed

• Stable by @JoQCcoz in #226
• Initial framework for CryoSPARC Live integration by @ccgauvin94 in #225
• Stable by @JoQCcoz in #227
• added download_testfiles command by @JoQCcoz in #228
• Add atlas_offset to the square acquisition by @JoQCcoz in #229
• Added ability to skip started targets. by @JoQCcoz in #230
• Stable by @JoQCcoz in #231
• Added stage limits by @JoQCcoz in #232

New Contributors

• @ccgauvin94 made their first contribution in #225

Full Changelog: 0.9.2-rc.2...0.9.2-rc.4

v0.9.2-rc.2

Main changes

• Added aperture controls for TFS microscopes
• Added Gridswapper for JEOL cryoARM microscope
• Added ability to automatically flash the cold FEG every X hours.
• Added REST API endpoints to upload highmag images and power spectrum and fetch detailed infomation about holes.
• Start of a big backend refactoring.

What's Changed

• Cli plot by @JoQCcoz in #197
• build development environment by @tiezheng-yuan-nih in #199
• default value of display_type by @tiezheng-yuan-nih in #200
• Cleaning up dev environment by @JoQCcoz in #203
• Svgrendering by @JoQCcoz in #206
• fixed read_config by @JoQCcoz in #207
• Dev by @JoQCcoz in #208
• fixed position of numbers in svg by @JoQCcoz in #209
• set environments with response to updates of Jo's dev branch by @tiezheng-yuan-nih in #210
• process higmag by @tiezheng-yuan-nih in #211
• example of unit testing by @tiezheng-yuan-nih in #216
• decouple autoscreen by @tiezheng-yuan-nih in #217
• Scopeinterface by @JoQCcoz in #218
• more debugging by @JoQCcoz in #219
• 0.9.2 rc.1 by @JoQCcoz in #220
• fixed ctf image not loading by @JoQCcoz in #221
• 0.9.2 rc.1 by @JoQCcoz in #222
• 0.9.2 rc.1 by @JoQCcoz in #223

New Contributors

• @tiezheng-yuan-nih made their first contribution in #199

Full Changelog: 0.9.1...0.9.2-rc.2

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

• fixed issue with missing method in fakescope by @JoQCcoz in #170
• Cli plot by @JoQCcoz in #171
• Cli plot by @JoQCcoz in #172
• Cli plot by @JoQCcoz in #173
• finalize preprocessing sidebar by @JoQCcoz in #174
• Fix issue with new version of chrome by @JoQCcoz in #175
• Dev by @JoQCcoz in #176
• EditcollectParams error by @JoQCcoz in #177
• added extra security to nginx config by @JoQCcoz in #178
• fix error in nginx ssl config by @JoQCcoz in #179
• Cli plot by @JoQCcoz in #180
• Fixed some issues with new preprocessing pielines by @JoQCcoz in #181
• Added more failsafes in smartscopePipeline by @JoQCcoz in #182
• fixed bug in smatscopePipeline by @JoQCcoz in #183
• Cli plot by @JoQCcoz in #184
• Dev by @JoQCcoz in #185
• fixed error in ai hole finder changes by @JoQCcoz in #186
• Cli plot by @JoQCcoz in #188
• Stable by @JoQCcoz in #205

Full Changelog: 0.9...0.9.1