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Tweak changelog and add MR list

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Co-authored-by: Beth Probert <beth_probert@outlook.com>
Co-authored-by: William Wadsworth <w.j.wadsworth@bath.ac.uk>
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Julian Stirling 2025-06-09 15:10:03 +00:00
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CHANGELOG.md
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# [v3.0.0-beta1](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v2.11.0...v3.0.0-alpha1)
# [v3.0.0-beta1](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v2.11.0...v3.0.0-alpha1) (2025-06-09)
This is the first alpha release of a almost total overhaul of the server, and the underlying LabThings framework. Some highlights are:
This is the first alpha release of an almost total overhaul of the server, and the underlying LabThings framework. Some highlights are:
* Moved to underlying architecture based on labthings-fastapi. This allows each component of the microscope to be a "Thing", which can interact with each other.
* Moved to underlying architecture based on [labthings-fastapi](https://github.com/labthings/labthings-fastapi). This allows each component of the microscope to be a "Thing", which can interact with each other.
* Current "Things" are camera, stage, autofocus, smart_scan background_detect, auto_recentre_stage, capture, settings_manager, system_control and test
* Overhaul of scanning, removing the predetermined, rectangular area in favour of exploring the sample indefinitely by appending neighbouring xy sites after each capture
* Background detect Thing optionally uses the colour distribution of a user-set "background" image to determine if the field of view is sample or background, and plan future scanning accordingly
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* Updated to numpy 2
* Automatically delete empty scans
V3 was started in a branch (MR !159)
The following merge requests have been merged into v3:
* !162 Scanning and recentring
* !163 Web app compatibility with v3 API
* !164 Modal progress dialog for TaskSubmitter
* !166 Pseudo spiral scan path and fixed dx-dy inversion
* !167 Restored old log path
* !168 Refactor task submitter
* !169 Run `openflexure-stitch` on the server
* !170 custom scan name from gui
* !171 Make it possible to manually save all settings to disk
* !172 Updates based on feedback from Rwanda trip
* !173 Autofocus efficiency
* !174 Parallel acquisition and moves
* !175 Improvements to autofocus and stitching in `smart_scan`.
* !176 Replace tasksubmitter with action-button
* !181 Add configurability to the server
* !191 Migrate to new Blob type and update imports
* !192 Formal Protocol for camera and stage interfaces
* !194 Add more unit tests and fix CI
* !226 Split up ruff format and lint
* !225 Rename exposure (with limit)
* !232 Purge all windows line endings and add check to formatter.
* !231 Reorder tabs
* !211 Use the UV channels only to determine if an area is background or sample
* !228 Stop uvicorn.run disabling existing loggers
* !227 CSM always returns to start on error
* !236 Inverse colours
* !239 Scanning cleanup
* !240 Refactor scanning
* !241 Add some extra rules to ruff, also add a more complete ruff config that fails
* !242 Further scan refactor
* !245 Add a scan path planner that prioritises shorter moves
* !247 Looping autofocus at the start of the scan
* !249 Remove focus_change_acceptable test
* !244 Remove correlation only stitching, now covered by preview stitch
* !250 Thumbnails and accurate durations in scan-list tab
* !253 Regex to count captured images
* !238 Disable tour
* !246 z stacking Thing
* !248 Cleanup zipping
* !255 Remove autofocus test
* !256 New comments on scanning
* !259 Update scan data JSON at end of scan
* !260 Scan tab updates
* !258 Use NumPy v2 and new wheel for opencv
* !230 Lazier regex for finding logs with square brackets
* !263 Clean up of serve_static_files
* !265 Update serve static files
* !267 Update theme.less to prevent automatic changed colour of uk-alert-success
* !268 GUI clean up - button cases, features tab and redo tour
* !269 Action buttons raise an Error from the last message in the log for the Actio
* !257 Added purge_empty_scans() method
* !270 Import openflexure-stitching from pip
* !272 Settling time as global, settle before taking first image in stack
* !261 CSM info in webapp tab
* !275 GUI shutdown clean up
* !276 Ui fixes
* !277 Fix error in purge_empty_scans if the `images` dir hadn't been created
* !266 Gui dzi viewer
* !278 update labthings-picamera to most recent release
* !279 Simulation fixes
* !281 Change from building with node 15 to node 18
* !282 Defocus and realign simulation axes
* !280 Custom `from_index()` function in webapp for backwards compatibility before javascrpt `at()`
* !284 Update labthings-api dep and also the version number for alpha release
* !286 Use same version number for server and webapp, add CI check
* !285 Swapped the order of CSM so y axis is completed first
* !283 Add scan directory to json config
* !287 Update depedencies and changelog prior to v3.0.0-alpha1 release
# [v2.11.0](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v2.10.1...v2.11.0) (2022-08-08)
## New features
* Background detection can now be used in scans, if you have the background-detect extension. ([!153](https://gitlab.com/openflexure/openflexure-microscope-server/-/merge_requests/153))