v0.5.8

What's Changed

• UI/new multipoint by @hongquanli in #333
• gui performance improvement: register fovs in batch by @Alpaca233 in #363
• Fix SimulatedCamera resolution calculation based on crop dimensions by @hongquanli in #368
• Filter wheel abstraction by @Alpaca233 in #359
• Fix the bug caused by repeated homing by @veerwang in #369
• Fix Laser AF exposure UI to use focus camera limits and laser AF calibration coefficient unit by @hongquanli in #371
• gui: add dialog for showing fovs to image in fluidics runs by @Alpaca233 in #373
• gui: 1536 well plate mouse selection by @Alpaca233 in #372
• bug fix: minor fix for #372 and #373 by @Alpaca233 in #375
• feat: save log in acquisition folder by @Alpaca233 in #374
• Install PyVCAM using pip by @GeekLogan in #377
• bug fix: switching to 1536 well plate by @Alpaca233 in #380
• Fix: Use camera exposure time in simulation mode by @hongquanli in #381
• feat: Add Skip Saving checkbox to multipoint acquisition widgets by @hongquanli in #383
• feat: Add RAM usage check for mosaic view before acquisition by @hongquanli in #382
• fix: Actually free RAM when clearing mosaic view layers by @hongquanli in #385
• fix: Replace napari icon and menu with Cephla's by @hongquanli in #388
• feat: Add Configuration dialog for editing settings via GUI by @hongquanli in #389
• fix: Resolve test segfaults / hang + Qt compatibility update + .pre-commit-config by @hongquanli in #391

New Contributors

• @GeekLogan made their first contribution in #377

Full Changelog: v0.5.7...v0.5.8

v0.5.7

What's Changed

• make control dock scrollable by @hongquanli in #332
• camera stress test: remove unused continuous, add binning, add bytes report by @ianohara in #334
• Revert "make control dock scrollable" by @hongquanli in #336
• fix: preserve channel metadata in multipage TIFFs via ImageDescri… by @hongquanli in #337
• Feature/add time and piezo to multipage tiff metadata by @hongquanli in #338
• feat: add OME-TIFF support by @hongquanli in #339
• remove SlidePositionController and SlidePositionWorker by @Alpaca233 in #324
• bug fix: buttons for coordinates are not disabled properly after acquisition is finished by @Alpaca233 in #342
• bug fix: Flexible Multipoint Widget by @Alpaca233 in #341
• feat: disable keyboard tracking on all spinbox widgets by @hongquanli in #344
• use same format for "Save Coordinates" and coordinates.csv in acquisition by @Alpaca233 in #343
• feat: set laser af reference when setting z min in z range by @Alpaca233 in #345
• bug fix: Flexible Multipoint importing/exporting list by @Alpaca233 in #346
• feat: Tucsen FL26 BW binning by @Alpaca233 in #348
• bug fix: toupcam resolution config by @Alpaca233 in #349
• remove some log info because it's taking too much disk space by @Alpaca233 in #351
• ux improvement: automatically stop live when doing laser af by @Alpaca233 in #354
• bug fix: laser power calibration by @Alpaca233 in #350
• workflow improvement: use z position from last timepoint to start autofocus during timelapse by @Alpaca233 in #353
• bug fix: z range initialization by @Alpaca233 in #352
• bug fix: Squid 6060 config by @Alpaca233 in #356
• feat: clear coordinates for navigation viewer by @Alpaca233 in #355
• bug fix: only the last manual region is shown on Navigation Viewer by @Alpaca233 in #357
• use variable sleep time to improve time lapse acquisition time resolution by @Alpaca233 in #358
• bug fix: missing live controller in well plate multipoint widget by @Alpaca233 in #361
• bug fix: move to piezo home position on start by @Alpaca233 in #360
• update default value for laser af settings by @Alpaca233 in #362
• bug fix: format of the coordinates file used for fluidics widget is different from the one in wellplate multipoint widget by @Alpaca233 in #364

Full Changelog: v0.5.6...v0.5.7

Known Issues

• Missing images in OME-TIFF on Windows

v0.5.6

What's Changed

• headless mpc: start pulling QT out of MultiPointController and Worker by @ianohara in #305
• MultiPoint*: Remove all QT usage, and cleanup unused/duplicate/broken abstractions by @ianohara in #304
• update Xeryon stage settings by @Alpaca233 in #311
• bug fix: Run Spot Detection by @Alpaca233 in #310
• feat: use software crop in AbstractCamera by @Alpaca233 in #309
• fixes: this fixes some issues with Microscope after all the qt-less refactoring by @ianohara in #313
• ScanCoordinates: Remove qt usage by @ianohara in #314
• ScanCoordinates: Consolidate SiLA2 scan coordinates functionality into a subclass by @ianohara in #315
• tools: get a basic microscope_stress_test working (with an acquisition) by @ianohara in #316
• fix naming typo: CELESTA config by @Alpaca233 in #312
• cameras: Tucsen Aries series support (genicam) by @Alpaca233 in #307
• move microcontroller initialization code out of gui by @Alpaca233 in #321
• bug fix: illumination always turns on when software starts by @Alpaca233 in #323
• update configuration file by @Alpaca233 in #325
• Andor camera, laser engine, and Dragonfly support by @Alpaca233 in #320
• update README by @Alpaca233 in #322
• update README by @hongquanli in #326
• update README images by @Alpaca233 in #327
• contrast autofocus: pull QT out of the base contrast and remove qt from related tests by @ianohara in #331
• microcontroller: force int as a bandaid, warn on non int arg to pid by @ianohara in #318
• bug fix: Calibration Live Viewer cannot be opened from Sample Format dropdown by @Alpaca233 in #328
• bug fix: laser af using other spots in averaging by @Alpaca233 in #329

Full Changelog: v0.5.5...v0.5.6

v0.5.5

What's Changed

• utils: TimingManager and Timer helper by @ianohara in #249
• microscope mode selection: do it directly, and only use signals for ui updates by @ianohara in #241
• MultiPointWorker: Use callbacks for image processing so we can trigger faster by @ianohara in #242
• mpw: remove blocking queue on qt signal by @ianohara in #248
• MultiPointWorker: Use trigger-time and move-time positions throughout. Do not recapture. by @ianohara in #250
• formatting: fix after merge train by @ianohara in #257
• close cameras explicitly on exit by @Alpaca233 in #255
• bug fix: Prior stage config update; Daheng camera model support by @Alpaca233 in #259
• z position plot error handling by @Alpaca233 in #260
• bug fix: gui connections for selecting microscope mode by @Alpaca233 in #263
• add Tenengrad focus measure option by @Alpaca233 in #258
• show a dialog for confirmation on close by @Alpaca233 in #264
• home x first to make sure stage is clear for homing by @Alpaca233 in #265
• fix test error caused by dialog window on close by @Alpaca233 in #266
• updated Tucsen FL26-BW camera support by @Alpaca233 in #267
• ui clean up: move some stage buttons to menu bar by @Alpaca233 in #268
• add a button to show/hide well selector by @hongquanli in #269
• line profiler - keep manual range if manual range is specified by @hongquanli in #270
• Octopi bug fix by @Alpaca233 in #271
• use characterization mode when laser af is not enabled by @Alpaca233 in #273
• startup xy and objective switcher sequence update by @hongquanli in #274
• gui: Make sure laser af attribs are set to none by @ianohara in #275
• cameras: default: fix strobe and exposure by @ianohara in #276
• Update Microscope class by @Alpaca233 in #277
• main_hcs: remove commented out code by @ianohara in #278
• apply gaussian filter before spot detection by @Alpaca233 in #280
• Gaussian filter fix by @Alpaca233 in #281
• gui: use the primary screen for initial window size by @ianohara in #279
• cameras: toupcam: fix timing to respect camera "trigger delay" and fix hardware triggering by @ianohara in #282
• MultiPointWorker: protect against in flight triggering by @ianohara in #283
• multi process jobs: Add in a job and job runner mechanism for processing images on separate processes by @ianohara in #285
• utils: Timer: print in insertion order, include total time, and right align by @ianohara in #284
• bug fix: update exposure time whenever trigger mode is changed by @Alpaca233 in #290
• bug fix: default trigger mode by @Alpaca233 in #286
• ux improvement: minor changes for multipoint acquisition widgets by @Alpaca233 in #291
• crop laser AF image before auto initialize by @Alpaca233 in #287
• bug fix: wellplate calibration widget by @Alpaca233 in #294
• bug: toupcam: do not double up on cam exposure time by @ianohara in #296
• acquisitions: wait for frames when using non-hw triggering by @ianohara in #288
• headless: reverse relationship between gui <-> microscope so we can have a truly headless api by @ianohara in #289

Full Changelog: v0.5.4...v0.5.5

v0.5.4

What's Changed

• snap image bug fix by @hongquanli in #238
• Binning and cropping in AbstractCamera class by @Alpaca233 in #217
• bug: fix crop_width and crop_height usage (they no longer exist) by @ianohara in #239
• logging: add thread id to our log lines by @ianohara in #240
• update camera model config and restore open camera by model by @Alpaca233 in #243
• camera bug fix: temperature reading; Hamamatsu model config; Squid configuration file by @Alpaca233 in #244
• use AbstractCamera class for Tucsen camera by @Alpaca233 in #246
• Hamamatsu camera: binning and resolution updates by @Alpaca233 in #247
• use AbstractCamera class for Kinetix camera by @Alpaca233 in #251
• cameras: Hamamatsu tested; add get_available_pixel_formats() by @Alpaca233 in #252
• add support for multi-page tiff by @hongquanli in #253
• fix Kinetix ROI by @Alpaca233 in #254
• camera fix: Kinetix camera set exposure time and Hamamatsu camera get exposure time range by @Alpaca233 in #256

Full Changelog: v0.5.3...v0.5.4

v0.5.3

What's Changed

• core: SlidePositionControlWorker: fix homing by @ianohara in #150
• fix ldi simulation mode not working by @hongquanli in #156
• attempt to fix software trigger freeze issue (not tested on hardware … by @hongquanli in #148
• add option for padding filename index with zeros by @Alpaca233 in #149
• Fluidics widget by @Alpaca233 in #154
• modify the filter wheel parameter value by @veerwang in #155
• gui: acquisitions: prevent acquisitions from starting if there is not enough disk space by @ianohara in #157
• update LaserAutofocusSettingWidget by @Alpaca233 in #160
• move back to region center after acquisition (for "glass slide" format) by @Alpaca233 in #161
• Kinetix camera support by @Alpaca233 in #162
• add reset_input_buffer in AbstractCephlaMicroSerial class and SimSeri… by @Alpaca233 in #167
• fix LaserAutofocusSettingWidget spinbox error by @Alpaca233 in #169
• Fixed Microscope class and made changes to MultiPoint Controller/Worker for headless mode by @Alpaca233 in #140
• remove default objective lens from configuration files by @Alpaca233 in #159
• fix piezo issue: acquisition always start from offset position rather than from laser af reference plane by @Alpaca233 in #166
• Kinetix camera: implement gain mode by @Alpaca233 in #170
• bug fix: acquisition stopped working after the last change - revert the change by @hongquanli in #174
• piezo bug fix by @Alpaca233 in #176
• add configuration variables requested by Arc Institute by @Alpaca233 in #177
• squid: abc: Add the AbstractCamera interface, and a simulated camera implementation by @ianohara in #61
• cameras: start plumbing AbstractCamera throughout by @ianohara in #111
• AbstractCamera: Add Toupcam implementation by @ianohara in #131
• cameras: add the default gxipy camera implementation by @ianohara in #145
• cameras: Add the Hamamatsu camera implementation by @ianohara in #151
• StreamHandler: allow providing an accept fn, and use it for the live controller by @ianohara in #178
• widgets: camera control: fix pixel format by @ianohara in #179
• formatting: fix formatting after merging all the camera prs by @ianohara in #180
• rm: delete hama test scripts by @ianohara in #181
• fix 1536 well plate error by @Alpaca233 in #158
• Update XLight iris diaphragm control by @Alpaca233 in #171
• feat: display z map post acquisition by @hongquanli in #182
• ensure 1:1 xy scale for z plot post acquisition by @hongquanli in #183
• cameras: None frame error universal, add test and test script by @ianohara in #186
• camera: simulated: fix continuous streaming mode, exposure, other by @ianohara in #187
• laser af microcontroller use: attempt to handle occasional timeouts by @ianohara in #168
• core&gui: cleanup, delete unused, and fix prints by @ianohara in #188
• microscope: fix CameraPixelFormat args by @ianohara in #189
• feat: add template multipoint by @hongquanli in #184
• Headless mode improvement by @Alpaca233 in #185
• restore DEFAULT_TRIGGER_MODE by @Alpaca233 in #191
• use get_channel_configuration_by_name by @Alpaca233 in #192
• use bottom z for z-surface plotting when z stacks are acquired by @hongquanli in #194
• workflows: main.yml: Fix headless qt setup by @ianohara in #197
• tests: skip debug plot test because backend by @ianohara in #198
• remove previous labels on changing to new laser AF profile by @Alpaca233 in #201
• Fix illumination/emission iris for Cicero by @Alpaca233 in #193
• tests: sim cam: force no flip or rotate by @ianohara in #202
• microscope: fix focus camera init to only be with focus cam by @ianohara in #203
• tools: add stage timing test script by @ianohara in #204
• firmware: calculate and put checksum in return packets by @ianohara in #195
• microcontroller: ignored packets with bad checksums, scan input buffer by @ianohara in #196
• Microcontroller: Add a read-staleness watchdog (sortof) so we can see if new data is coming in by @ianohara in #199
• microscope: Eliminate 1 move in z backlash compensation by @ianohara in #190
• tools: stage timing: allow any axis, start and step, no home by @ianohara in #206
• microcontroller: use a cv for wait instead of sleep and poll by @ianohara in #205
• z movement: move backlash compensation into CephlaStage so it is universal by @ianohara in #207
• stage: cephla: change backlash comp from 30um to 5um for speed by @ianohara in #208
• microscope: fix incorrect _log attribute use and init order by @ianohara in #210
• Focus map improvement by @Alpaca233 in #175
• fix SpotDetectionMode value error by @Alpaca233 in #212
• export and import focus points by @Alpaca233 in #213
• feat: add output power linearization for Squid LED/Laser (PM16 from Thorlabs needed) by @hongquanli in #214
• bug fix for PR #175, #214 and a few other improvements by @Alpaca233 in #218
• save coordinates for all objectives by @Alpaca233 in #222
• revert the change in LaserAFConfig base model by @Alpaca233 in #221
• keep manual ROI after clearing mosaic view by @Alpaca233 in #220
• fix emergency stop for fluidics widget by @Alpaca233 in #219
• core: MultiPointWorker: separate into its own file by @ianohara in #223
• MultiPointWorker: Delete unused code paths by @ianohara in #224
• cameras: toupcam: allow ignoring default black level by @ianohara in #225
• MultiPointController: Add type annotations, cleanup names where risk-free by @ianohara in #226
• MultiPointController: remove a few risk free unused bits by @ianohara in #227
• illumination control bug fix: setting current channel by @Alpaca233 in #229
• add status bar to live display to show cursor pixel value and stage position by @hongquanli in #230
• add the ability to snap multi channel images of the current FOV by @hongquanli in #231
• show napari status bar for displaying pixel value by @hongquanli in #232
• add line profiler by @hongquanli in #233
• pixel value display int instead of float, no display when cursor off image by @hongquanli in #234
• simulation bug fix (CrestOptics and LDI) by @hongquanli in #235

Full Changelog: v0.5.2...v0.5.3

v0.5.2

What's Changed

• major update: add channel configuration file management by @Alpaca233 in #100
• PR#100 merge bug fix by @hongquanli in #115
• add objective mag in napari layer name by @hongquanli in #118
• starting to remove display resolution scaling by @hongquanli in #119
• update laser autofocus implementation for loading settings for different objectives by @Alpaca233 in #117
• run black on the repo by @hongquanli in #120
• feat: Add save/load scan coordinates to CSV in the GUI by @hongquanli in #116
• new Piezo class related bug fix by @hongquanli in #121
• fix missing import / passing wrong object by @hongquanli in #122
• bug fix - wrong function was called for piezo.position() by @hongquanli in #123
• fix: handle piezo presence/absence by @ianohara in #124
• fix: daemonize process queue threads so we get clean close even if signals are missed. by @ianohara in #125
• feat: enforce laser autofocus reference requirement by @hongquanli in #127
• Improve Laser-Based Focus display to show results of running laser autofocus by @Alpaca233 in #126
• run black by @hongquanli in #128
• fix(logging): Make sure our file handler uses unicode and continues through errors by @ianohara in #130
• laser af improvement (remove background for initial spot localization) by @hongquanli in #133
• laser autofocus bug fix (widget and display related) by @Alpaca233 in #129
• laser autofocus UX improvement by @Alpaca233 in #134
• Save / load laser af reference image as part of cached laser af profile by @Alpaca233 in #132
• fluidics integration by @hongquanli in #114
• fix(tests): microscope init test fix, other argument change fixes by @ianohara in #136
• Ian/you yan celesta logging fix by @hongquanli in #138
• fix for acquisitions without laser af by @Alpaca233 in #139
• bug fix: channel colormap and configuration manager connections by @Alpaca233 in #135
• bug fix: multipoint controller and well selector by @Alpaca233 in #141
• stage + gui: set limits, and fix limit direction bug by @ianohara in #142
• gui: drive y+20, x+20 before homing x+y to make sure we are clear by @ianohara in #144
• update default channel config by @Alpaca233 in #146
• bug fix: focus map for glass slide by @Alpaca233 in #147

Full Changelog: v0.5.1...v0.5.2

release before adding channel config files management (for different objectives)

What's Changed

• feat: improve laser autofocus with robust spot detection and error handling by @hongquanli in #101
• feat: improve piezo stage control by @hongquanli in #106
• pull from master by @hongquanli in #107
• bug fix by @hongquanli in #108
• bug fix for updated laser autofocus by @hongquanli in #109
• fix: for both config editors, catch and alert on file permission errors by @ianohara in #105
• fixes(tests): move tests to existing location, fix (or ignore) broken tests by @ianohara in #110
• laser af init bug fix by @hongquanli in #113

Full Changelog: v0.5...v0.5.1

v0.5 - release before updating laser af

What's Changed

• logging: add logging mechanism, hooks to log uncaught crashes, and an example use of the logging tools by @ianohara in #1
• software/main_: Delete unused imports, convert the main and gui to use loggers. by @ianohara in #4
• control/microcontroller: convert to using Logger and remove some unused/commented code by @ianohara in #5
• logging: add a helper for registering a rotating file log that captures all output regardless of stdout log level by @ianohara in #6
• control/camera_toupcam: use loggers by @ianohara in #7
• logging: add missing close quote in logging message by @ianohara in #8
• gitignore: add .idea/ directories. by @ianohara in #9
• Merge hongquanli/octopi-research/master and fix conflicts by @ianohara in #16
• microcontroller: fix reset cmd_id bug by @ianohara in #10
• microcontroller: combine the move commands via a helper by @ianohara in #11
• microcontroller: for simulation, use a stub serial device instead of copy/pasted implementation by @ianohara in #12
• microcontroller: add the notion of aborted commands, and throw TimeoutError on failed waits by @ianohara in #13
• gui_hcs: if the microcontroller times out during initialization, reset it before failing by @ianohara in #14
• firmware: fix bug where hardware trigger interrupt was able to access partially written data by @ianohara in #15
• Merge octopi-research/master (click to move update and sample format bug fix) by @hongquanli in #17
• sample format bug fix (glass slide) by @hongquanli in #18
• restore x,y,z position update in simulated microcontroller by @hongquanli in #21
• click-to-move in navigationViewer by @sohamazing in #19
• click-to-move navigation viewer offset by @sohamazing in #23
• manually merge commits from Soham (mostly sample format related bug fix) by @hongquanli in #25
• setup and cleanup: fix setup scripts for new repo, delete outdate and move tools. Add action for install + tests. by @ianohara in #31
• microscope: fix simulated mode in microscope by @ianohara in #32
• Flexible scan grid by @sohamazing in #27
• Hamamatsu hardware trigger bug fix by @Alpaca233 in #26
• add support for celesta by @hongquanli in #41
• microcontroller: remove is_simulated at Microcontroller level, and instead implement simulated firmware at Serial level by @ianohara in #33
• tracking: remove unused and incomplete tracking implementations. Those in core.py and widgets.py stay. by @ianohara in #43
• update live scan grid: delay live scan grid generation when xy-stage moving, init live scan grid to 1mm by @sohamazing in #36
• signal cleanup: remove redundant signals, streamline acquisition signal and slot logic by @sohamazing in #37
• bug fix: edits to manual region shape should not update scan coordinates while on flexible widget by @sohamazing in #38
• cleanup: remove tileddisplaywidget and multipointwidget and cleanup spaces by @sohamazing in #39
• Pr filterspin by @veerwang in #46
• pulled out region_coordinates from MultiPointWidgets into ScanCoordinates by @sohamazing in #47
• interface: start pulling out the stage concept by @ianohara in #34
• stage: integrate into the system (replace NavigationController) by @ianohara in #48
• IlluminationController class initial commit by @Alpaca233 in #42
• interface: start pulling out illumination control by @hongquanli in #54
• add support for celesta by @hongquanli in #40
• add manual focus map function by @hongquanli in #56
• add manual focus map by @hongquanli in #57
• focus-map: (manual focus point grid) - specify z level at points, fit to 3d surface, interpolate for acquisition scan fovs by @sohamazing in #50
• fix bug comes from merging code by @veerwang in #55
• fix: celesta should be off by default by @ianohara in #58
• fix: send pos from movement updater, and start movement updater by @ianohara in #59
• formatting: format entire repo with black by @ianohara in #49
• fix: scan coordinate preview by @hongquanli in #62
• improvement: prevent constant update of scan coordinate preview by @hongquanli in #63
• Prior stage with abstract stage class by @Alpaca233 in #65
• fix a bug of axis move direct by @veerwang in #66
• Prior stage bug fix by @Alpaca233 in #67
• fix(microcontroller): microcontroller test rel moves are correct now by @ianohara in #70
• Focus map refactoring by @Alpaca233 in #69
• fix(core): remove duplicate initializations by @ianohara in #72
• fix(lint action): Fail linting action if formatting would have happened by @ianohara in #73
• fix(formatting): Run black on whole repo again to get to clean lint state by @ianohara in #74
• debug(laser af): only catch Exception, print exec_info, indicate failure for caller in autofocus method by @ianohara in #75
• fix(acquisition abort): Aborting acquisitions midway left the ui in an invalid state by @ianohara in #76
• fix(MultiPointWorker): logging in update_use_piezo had a missing format in string by @ianohara in #77
• acquisitions: catch TimeoutErrors in acquisitions, and abort acquisition cleanly by @ianohara in #81
• utils: add a directory creation helper, and use it instad of os.mkdirs by @ianohara in #82
• feature: add Jupyter console by @hongquanli in #71
• 2 position objective changer by @Alpaca233 in #83
• New scan shape: Rectangle by @Alpaca233 in #85
• add auto offset adjustment for objective switching by @hongquanli in #87
• Fix LDI laser engine errors caused by IlluminationController by @Alpaca233 in #86
• fix(stage): pass in PriorStage config when using Prior by @ianohara in #88
• stage: prior: add a position polling timer by @ianohara in #91
• manual roi: fix incorrect index by @ianohara in #92
• prior: use a thread instead of timers by @ianohara in #93
• manual regions: add corner check for inclusion criteria by @ianohara in #95
• feat(microcontroller): Add a mechanism for automatic serial reconnect, and use it by @ianohara in #78
• make the downsampling in mosaic view scale with objectice mag by @hongquanli in #94
• acquistions: when we abort, do not let another start until previous is finished by @ianohara in #96
• fix: move lighting tools to their own module to avoid circular import by @ianohara in #89
• objective switcher init bug fix by @hongquanli in #99
• manual focus map improvements by @Alpaca233 in #98
• fix: napari init attrib bug, and add unit tests by @ianohara in #102
• logging&utils: add helper for getting squid repo state, log state on startup by @ianohara in #103
• simulated micro: fix to be thread safe by @ianohara in #104

New Contributors

• @sohamazing made their first contribution in #19
• @Alpaca233 made their first contribution in #26
• @veerwang made their first contribution in https://github.com/Cephla-Lab...