Release Notes

Next Release


  • Explicitly reference license in project README and generated documentation main page. #227

  • Fix documentation generation adding .readthedocs.yaml to explicitly desxcribe the documentation build environment. #227

Cell Locator 0.3.0-2022-07-25


  • Add structure ID and acronym to JSON format. #208

  • Add optional lims-specimen-kind command line parameter. #213


  • Don’t show exit confirmation when file (or LIMS specimen) is unchanged. #204


  • Document double-click action to rename annotations. #206

  • Update expected Slice Offset values in QA template. #203; see #139 (comment) for details.

Cell Locator 0.2.0 2021-08-12


  • Created script to convert between Cell Locator file formats. #181, #182


  • Fixed new "measurements" key being incorrectly included in serialization. #182

  • Fixed changing ontology resetting slice view. #178

  • Fixed GUI desync when editing multiple annotations. #179, #180

  • Fixed polyline annotations incorrectly loading as splines. #184

  • Fixed point annotations persisting after scene clear. #185


  • Document the Annotation type hierarchy.

  • Provide documentation and example of how to create new Annotation types.

  • Document the mock LIMS server and LIMS API.

  • Switch from recommonmark to MyST; so that reStructuredText may be avoided entirely. See Slicer#5662.

  • File Format Version bumped to 0.2.0+2021-08-12 #198

Cell Locator 0.1.0 2021-05-21


  • Add support for adding “point” annotations. See #164 and #164.

  • Add support for user selection of atlas through the UI at startup if no atlas is specified on the command line. See #165

  • Add a version number to the file format using semantic versioning. See #170


  • Fix orientation of MNI atlas. See #163

  • Use full annotations for MNI atlas, instead of single side annotation. See #164

  • Fix errors when changing interaction mode while there are no annotations in the scene. See #173


Cell Locator 0.1.0 2020-09-18


  • Add support for editing multiple annotations in one file. See #90

    • List of annotations displayed on left sidebar.

    • Add button for adding, cloning, and removing? annotations. See #102

  • Responsive UI depending on whether CellLocator was launched by LIMS

    • If launched with LIMS enabled, hide the file controls (New, Save, Load, Save As). Otherwise, hide the LIMS controls (Save to LIMS)

  • Save and load annotations by name

    • Double-click annotation to rename

  • Display interaction handles allowing to rotate or translate current annotation. See #141 and #118

  • Display error dialog when LIMS connection failed to be established.

  • Add support for loading MNI atlas. See #99

    • Accept --atlas-type command line argument.

    • Supported value for atlas type are mni and ccf.

    • Display mm unit suffix for mni atlas and um for ccf atlas.

File format:

  • Simplify annotation format removing unneeded keys. See #150


  • Drawing a second polygon results in an empty json file. See #108

  • Use of contrast “reset” button. See #136

  • Use of Ctrl+W shortcut to reset application state. See #134

  • Crash on application shutdown. See #154

  • Remember last saved directory. See #137

  • Initialize annotation base name to Annotation instead of MarkupsClosedCurve.

  • Ensure only current annotation can be updated when annotate or place mode is activated.

  • Hide irrelevant annotation control point right click menu entries.

  • Handle annotation payload with missing data key.

  • Fix annotation scaling. See #156

  • Spline polygons do not save, but also do not disappear in a session involving multiple files. See #112

  • After using Ctrl+w and restarting the application, mm unit prefix is displayed instead of um. See #89

  • Support loading annotation from network path. See #103


  • Add with Making a release section.

  • Update Keyboard Accelerators and Mouse Operations / Annotation section in


Cell Locator 0.1.0 2020-08-26


  • In addition of Explore and Annotate mode, introduce the Place interaction mode.

    • Annotate: Used for editing existing control points.

    • Place: Used for adding new control points

    • Explore: Used for exploring the space



  • Improve LIMS integration to address the feedback in #93.

    • Switch to the requests library to properly handle request headers. POST requests use the json argument, which sets Content-Type: application/json.

    • Change failure messages to be more helpful. Now includes the error status code and message. For example: Failed to load annotations for LIMS specimen <ID>. Error <STATUS>: '<REASON>'

    • Current LIMS specimen ID is shown in the file path box below “Save to LIMS”.

  • Ensure updating annotation point do not move the whole polygon. See #109

  • Improve insertion of point in existing annotation. See #80

Cell Locator 0.1.0 2020-07-30


  • Add LIMS support. See #93

    • Support command-line flags --lims-specimen-id and --lims-base-url.

    • Add new section to README


Cell Locator 0.1.0 2020-04-30


  • Add support for --reference-view, --view-angle and --annotation-file command-line arguments. See #97


  • Ensure that +x is +P in both slice view and 3D view. See #101

  • Ensure load dialog is associated with directory last used for loading. See #105

Cell Locator 0.1.0 2020-04-16


  • Ensure Coronal referenceView is coherent between 2D and 3D view. See #101

Cell Locator 0.1.0 2019-06-03


  • Reset camera position on reset. See #71

  • Leave the camera alone when creating a new annotation. See #70 Motivation: better workflow for pinning multiple cells to the same slice

  • Add a window/level slider for the background image. See #69

  • Enable 2D Viewer pan and zoom. See #68

  • Support for loading an annotation using Ctrl+O shortcut

  • Support saving of view properties even if no annotation was added


  • Add “Known Issues” section to README

  • Add issue templates for QA, feature request and bug report

  • Update “Keyboard Accelerators and Mouse Operations”


  • Ensure referenceView is not reset when adding point to an annotation. See #72

  • Ensure entering Roll/Pitch/Yaw values does NOT automatically Apply. See #75 and #67

  • Ensure Sagittal referenceView is coherent between 2D and 3D view. See #74

  • Fix handling of New/Save/SaveAs/Load. See #65

  • Fix “Load -> Cancel -> SaveAs” workflow. See #86

  • Disable unneeded keyboard shortcuts in 3D viewer

  • Update roll/pitch/yaw slides to use single step of 1 and pageStep of 5. See #82

  • Only associate Unit prefix with StepSize and Thickness sliders

  • Ensure loaded annotation are snapped when switching to edit mode

  • Ensure load dialog is associated with directory last use for saving. See #85

Cell Locator 0.1.0 2019-02-19


  • Add “Keyboard Accelerators” section to README


  • Rename S/I axis to D/V. See #66

  • Fix transparency of application windows icon. See #66

  • Set dialog title when creating new annotation. See #66

  • Improve logo. See #13

  • Ensure launcher splashscreen remains visible

Cell Locator 0.1.0 2019-02-15


  • Improve handling of default save location. By default, the “Documents” location is used. In subsequent save operation, the last known saved directory is suggested. See #62

  • Do not keep track of last annotation save directory if unsuccessful saving. See #62

  • Re-order orientation sliders

  • Ensure the “Apply” button is always enabled when setting roll/pitch/raw

  • Ensure slice orientation is restored when loading annotation

  • Update SplashScreen, logo and icon. See #13

Cell Locator 0.1.0 2019-01-26


  • Add support for changing annotation type from “spline” to “polyline”. #57

  • Support selecting “None” Color. See #61

  • Pretty-print serialized annotation file. See #63

  • Add reset field of view button. See #64

  • Serialize ReferenceView, StepSize, Ontology and Camera Position&ViewUp in annotation json file. See #22

  • Add Ctrl+N, Ctrl+S and Ctrl+W shortcuts

  • Do not require user to click “New” after starting the application


  • Ensure the selected annotation point is removed. See #42

  • Prevent downsizing of “New” icon

  • Ensure interaction state is always up-to-date

  • Improve state management of Apply, Reset and orientation sliders. Enable or disable the widget if appropriate.

  • Ensure thickness is set after loading annotation

  • Fix crash when loading -> closing scene -> loading

  • Properly handle of view Reset without Apply

  • Ensure stepSize slider singleStep is set

  • Fix handling of interaction state to support “annotate” mode after loading

Cell Locator 0.1.0 2019-01-21

  • Initial Release