Release Notes
Next Release
Documentation:
Cell Locator 0.3.0-2022-07-25
Features:
Add structure ID and acronym to JSON format. #208
Add optional
lims-specimen-kind
command line parameter. #213
Fixes:
Don’t show exit confirmation when file (or LIMS specimen) is unchanged. #204
Documentation:
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
Features:
Fixes:
Fixed new
"measurements"
key being incorrectly included in serialization. #182Fixed 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
Documentation:
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
Features:
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
Fixes:
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
Documentation:
Add Documentation/CoordinateSystem.md with
Updates
section.Add versioning history to Documentation/AnnotationFileFormat.md. The current version is
0.1.0+2020.09.18
Cell Locator 0.1.0 2020-09-18
Features:
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
andccf
.Display
mm
unit suffix formni
atlas andum
forccf
atlas.
File format:
Simplify annotation format removing unneeded keys. See #150
Fixes:
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 ofMarkupsClosedCurve
.Ensure only current annotation can be updated when
annotate
orplace
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 ofum
. See #89Support loading annotation from network path. See #103
Documentation:
Add MAINTAINERS.md with
Making a release
section.Update
Keyboard Accelerators and Mouse Operations / Annotation
section inREADME.md
.
Testing:
Update AllenInstituteMockLIMS adding Getting Started section to
README.md
.
Cell Locator 0.1.0 2020-08-26
Features:
In addition of
Explore
andAnnotate
mode, introduce thePlace
interaction mode.Annotate
: Used for editing existing control points.Place
: Used for adding new control pointsExplore
: Used for exploring the space
Infrastructure:
Update Slicer to version from 2020-08-14. See KitwareMedical/Slicer@cell-locator-v4.11.0-2020-08-14-376d405c2b and #96
Update to Python 3
Introduce
Annotation
andAnnotationManager
classes for interfacing with built-in Slicer markups nodes.
Fixes:
Improve LIMS integration to address the feedback in #93.
Switch to the
requests
library to properly handle request headers. POST requests use thejson
argument, which setsContent-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
Features:
Add LIMS support. See #93
Support command-line flags
--lims-specimen-id
and--lims-base-url
.Add new section to README
Tests:
Add mock server to test LIMS functionalities. See instructions at https://github.com/KitwareMedical/AllenInstituteMockLIMS
Cell Locator 0.1.0 2020-04-30
Features:
Add support for
--reference-view
,--view-angle
and--annotation-file
command-line arguments. See #97
Fixes:
Cell Locator 0.1.0 2020-04-16
Fixes:
Ensure Coronal referenceView is coherent between 2D and 3D view. See #101
Cell Locator 0.1.0 2019-06-03
Features:
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
shortcutSupport saving of view properties even if no annotation was added
Documentation:
Add “Known Issues” section to README
Add issue templates for QA, feature request and bug report
Update “Keyboard Accelerators and Mouse Operations”
Fixes:
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
Documentation:
Add “Keyboard Accelerators” section to README
Fixes:
Cell Locator 0.1.0 2019-02-15
Fixes:
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
Features:
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
andCtrl+W
shortcutsDo not require user to click “New” after starting the application
Fixes:
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