TrackMate v9 - #353

Draft

tinevez wants to merge 376 commits into

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Commits on Jun 29, 2026

Show spots without meshes as icosahedron spheres.
tinevez
committed
f94d305
Don't crash when loading faulty meshes.
tinevez
committed
20265b2
Fix OverlapTracker not working if the first frame was devoid of visible spots.
tinevez
committed
a87b605
Put a test drive in a try/catch block so that we can get exceptions.
tinevez
committed
97fdb8b
Minor tweak of the demo.
tinevez
committed
6738b29
Reflect model edits in the TrackMate-BVV.
tinevez
committed
1d615a9
TrackMate BVV can focus view on selected spot.
tinevez
committed
41cf2cb
Basic support of selection highlighting in the BVV.
tinevez
committed
5979ad3
Add a button to launch a 3D view on the GUI.
tinevez
committed
c463b8e
Tweak error messages.
tinevez
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785ea9c
WIP: rework the 2d + z processor.
tinevez
committed
8746328
Fix a very serious and a very stupid mistake with the move() methods of Spot.
tinevez
committed
425db02
Make the meshToSpot method public.
tinevez
committed
47b6e77
WIP: on Process2DZ, assign quality, work well with ROIs.
tinevez
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4fafc65
Disable GUI when launching BVV.
tinevez
committed
95557bd
Simplify StupidMesh.
tinevez
committed
e5d9f51
Exposes the BvvHandler of a TrackMate BVV view.
tinevez
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a0d0bf5
Set frame title of TrackMate BVV views.
tinevez
committed
b30793a
Position the BVV window more or less next to the GUI.
tinevez
committed
ffabe88
Better return signature for mesh to spot mesh method.
tinevez
committed
d992fb9
Make sure we have a SpotMesh built with all normals computed.
tinevez
committed
7148c33
Tweak the Process2DZ detector.
tinevez
committed
b5f78b8
Update to non-SNAPSHOT version of bigvolumeviewer.
tinevez
committed
47d0429
WIP: Trying to implement transparency of meshes.
tinevez
committed
812c2ab
Fix cast error
tinevez
committed
2e54332
Spot is now an interface, with 3 derived class.
tinevez
committed
52938c8
Rework the 2D and 3D detection utils.
tinevez
committed
cc2cf0c
WIP show meshes in bvv. requires 'mesh' branch of bvv

tpietzsch
authored and
tinevez
committed
7b72c8b
Depend on imglib2-mesh preview, not on net-imagej-mesh.
tinevez
committed
395834a
Use the scale method of the spot interface.
tinevez
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4be3e46
Don't hide exceptions when launching the BVV.
tinevez
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1c96be7
Try to do without deprecated method.
tinevez
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619a43d
Remove debug main method.
tinevez
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89ed861
Use the new imglib2-mesh master branch in the imglib2 org.
tinevez
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82b6363
Abide to recent changes in imglib2-mesh.
tinevez
committed
9aa5b4a
Fix all javadoc warnings.
tinevez
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0f00eb2
Fix mistake in calling the translateScale mesh method.
tinevez
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98b7797
Make the mesh of a SpotMesh setable.
tinevez
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ce14c2c
Return the actual BufferMesh class when we expose the mesh of a SpotMesh.
tinevez
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72cde37
Display the default element in the enum combobox of StyleElements.
tinevez
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802f410
An action to smooth meshes with Tuabin smoothing.
tinevez
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e51487e
Multithread the mesh smoother.
tinevez
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b20c366
Improve smoothing action.
tinevez
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32b6d10
Mesh smoother can run on all visible spots or only on selection.
tinevez
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8d7c819
Tweak the mesh smoother panel.
tinevez
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1cf63d5
Tell the user when we update meshes and features after smoothing meshes.
tinevez
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cfc8018
Add a toString method to MeshSmootherModel.
tinevez
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6bce463
Add a 'basic' setting panel to the mesh smoother.
tinevez
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16b881c
The mesh smoother uses the numThreads from the trackmate instance.
tinevez
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778911a
WIP: Smooth mask or label before generating mesh to smooth it.
tinevez
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7fcf063
WIP: Implement smoothing in threshold and mask detectors.
tinevez
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5a86bba
Optionally check for the presence of a parameter in a settings map.
tinevez
committed
4c5eb62
Tweak the slider panels.
tinevez
committed
3e8e882
fix the PanelSmoothContour.
tinevez
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0ca14df
Implement smoothing of images before segmentation.
tinevez
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f7e5ee4
Implement the smoothing scale in the threshold, mask and label detectors.
tinevez
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9fc05e9
setFont() for the slider panels.
tinevez
committed
4d3af54
Fix incorrect documentation.
tinevez
committed
21ce5db
Fix compile error due to casting error.
tinevez
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b0d6725
Move the shader files to the resources folder.
tinevez
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bb1a244
Handle whether we have or have not channels with the Process2DZ.
tinevez
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2f20b80
Fix handling of ROIs in Process2DZ with multiple channels.
tinevez
committed
b9ccb2c
WIP show meshes in bvv. requires 'mesh' branch of bvv

tpietzsch
authored and
tinevez
committed
4d23401
Add a button to launch LabKit in the configure views panel of the wizard.
tinevez
committed
abb645f
Try to fix LegacyService error.
tinevez
committed
f4efef8
Fix reimporting labels with large IDs in 2D.
tinevez
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b2bee96
Don't go out of bounds when measuring spot quality in 2D.
tinevez
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3a80cef
Fix the legacy error issue?
tinevez
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da483ba
The quality image in from2DThresholdWithROI is of RealType.
tinevez
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9b86355
All labeling methods now use the double[] origin to reposition spots.
tinevez
committed
c0a9fad
Update license blurbs.
tinevez
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7b4d0db
Temporarily disable enforcer checks.
tinevez
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ec6246c
The Process2DZ detector is cancelable.
tinevez
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195d762
POM: fix the dependencies

ctrueden
authored and
tinevez
committed
1cacb59
Fix Javadoc errors

ctrueden
authored and
tinevez
committed
b9ba926
A utility widget to specify a threshold on a probability value.
tinevez
committed
91d254d
Clamp slider widget values.
tinevez
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dd073a3
Add required methods in SpotRoiUtils.
tinevez
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e977d06
Don't crash if the saved tracker is unknown to us.
tinevez
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061da4d
Add a methods to return the map of label to spots in a labeling image.
tinevez
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f8a41cd
Add the smoothing scale param to the 2D labeling methods as well.
tinevez
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cde3735
Remove unused methods.
tinevez
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331da00
Update devel TrackMate major version number to 9.
tinevez
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bce24f4
Protect is someone asks the nD (n>2) bounds of a 2D spots.
tinevez
committed
dae89ef
Put back the createROIInterval method that went with the big rebase.
tinevez
committed
587fe8e
Fix the spot boundingBox method in the Labkit editor.
tinevez
committed
0a645c2
Fix the spot iteration for Labkit model.
tinevez
committed
e8f2857
Fix the MaskUtils.fromThresholdWithROI calls with TrackMate v9
tinevez
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a222848
Fix javadoc warnings and errors.
tinevez
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56742af
Fix the mask, threshold and label image detector config panel layout.
tinevez
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ab48d71
Put back missing clearEnvMap() method.
tinevez
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ec38635
Remove unused dependencies
tinevez
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90c8597
Update parent to pom-scijava v45.0.0
tinevez
committed
f62a522

Commits on Jul 1, 2026

Allow de/serializing enum parameters.
tinevez
committed
10ff313

Commits on Jul 2, 2026

Add config-ui as a dependency.
tinevez
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3722de3
An intermediate class For TrackMate modules using Configurator.
tinevez
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5e4e2ab
A generic detector config panel using config-ui Configurator.
tinevez
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1c4edb7

Commits on Jul 4, 2026

Commits on Jul 5, 2026

Interfaces for detector and tracker factories that use a Configurator.
tinevez
committed
1c8b83b
The LoG, DoG and Hessian detector now use the new Configurator.
tinevez
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dfd1393
Remove the CLI Configorator classes of TrackMate v8.
tinevez
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26dc982
Don't crash the generic config panel if there are no icon.
tinevez
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a5fdda0
Use reorder in the Hessian detector Configurator.
tinevez
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297d931
Don't limit the size of the info display in generic config panel.
tinevez
committed
cdd0279
Fix th configs for the LoG, DoG and Hessian detector.
tinevez
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bd2abb6

Commits on Jul 7, 2026

Fix smoothing scale being ignored for 2D images.
tinevez
committed
0a035c7

Commits on Jul 19, 2026

Commits on Jul 26, 2026

Don't add a MouseAndKeyHandler twice.
tinevez
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5f6b6d7
Interface for commands with undo / redo
tinevez
committed
f9505b0
Code style changes.
tinevez
committed
14d1839
Use TMImageLabelingModel when we can.
tinevez
committed
8db8fa8
Undo / redo for the edits made with the brush.
tinevez
committed
e968b0c
Use the TMImageLabelingModel type in flood fill controller
tinevez
committed
ec6b63f
D'oh! Method signature should be for Interval not FinalInterval.
tinevez
committed
d18d119
A modification of imglib2 FloodFill to return the the bounding-box of the filled region.
tinevez
committed
11d9ab2
Undo / redo for the flood fill operations.
tinevez
committed
f7ba04d
Fix editor bugs with ROI editing and editing outside the image.
tinevez
committed
77b01c1

Commits on Jul 27, 2026

Ensure undo process consistency.
tinevez
committed
723b2f5
Message the user about undo / redo.
tinevez
committed
2cbe923
D'oh!
tinevez
committed
bdf07f6
Fix performance issue when removing with the brush.
tinevez
committed
b0be5c6

Commits on Jul 28, 2026

WIP: Testing undo / redo for the main Model.
tinevez
committed
a1dbc03
Don't record undo when loading a model.
tinevez
committed
d09349a
Plug undo / redo into the ImageJ view.
tinevez
committed
64c1eb1
Allow modifying the polygon of a SpotRoi.
tinevez
committed
1ad5272
Undo / redo can restore spot position and radius.
tinevez
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60044a4
Undo / redo also restores feature of edges that were modified
tinevez
committed
faa068a
Implement undo / redo in the TrackScheme JFrame.
tinevez
committed
a1138c2

Commits on Jul 29, 2026

Undo / redo spot name changes.
tinevez
committed
fe62430

Commits on Jul 30, 2026

Simplify flagging a spot for update.
tinevez
committed
57fc946
Add undo / redo on all views and wizard window.
tinevez
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84d4231
Undo / redo only follow model modification events.
tinevez
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bc373f5
Release constraint on getSpotAt() method of SpotCollection.
tinevez
committed
7cca8bf
The scale() method of Spot also updates the RADIUS feature.
tinevez
committed
db038ad
Try to build a 'thing' that adapt ui-behaviour to AWT canvas.
tinevez
committed
1290d9f
WIP: Toy with the UI behaviour framework in the HyperstackDisplayer.
tinevez
committed
38d54c1

Commits on Jul 31, 2026

Code style changes.
tinevez
committed
07e385a
Create a reversed DFS for the track model.
tinevez
committed
1e0c283
Add methods to navigate to a root an to a leaf of a track.
tinevez
committed
e01cecc
Move the spot edit bahviour classes inside a utility class.
tinevez
committed
eead567
Move the AbstractSpotEditBehaviour to its own class.
tinevez
committed
4c72244
A drag behaviour, to toggle links between spots.
tinevez
committed
89f300f
Add and register behaviours to add, delete and link spots.
tinevez
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309e5af
Add actions that for several edit actions.
tinevez
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024e912
Actions to change timepoints.
tinevez
committed
2ab2c90
Spot selection and semi-auto tracking.
tinevez
committed
4b9498a
Select spots with the FreehandRoi, no need for a special IJ tool.
tinevez
committed
7e73ae8
Remove duplicate class.
tinevez
committed
bb4f368

Commits on Aug 1, 2026

Make key bindings documented and editable via a Preferences dialog.
tinevez
committed
b27fe30
A specific KeymapManager for TrackMate.
tinevez
committed
79b221e
Refactor: a class that adapts ui-behaviour to an ImagePlus.
tinevez
committed
b729662
Store the TrackMateKeymapManager as a static instance.
tinevez
committed
ee4053b
Refactor: use the new ui-behaviour classes in the main view.
tinevez
committed
1efb628
Remove the old spot edit tool 🥳
tinevez
committed
8bc69b1
Put all key config contexts and scope in one file.
tinevez
committed
def7ae6
Extract general actions to a class.
tinevez
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67a4041
Serialize keymaps.
tinevez
committed
08c5cac

Commits on Aug 2, 2026

Also remove the old ModelEditActions
tinevez
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5aef0d3
Remove the editingSpot from the overlay.
tinevez
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5ca11c2
Remove the solo undo / redo keybinding.
tinevez
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02f44df
Put the TrackMateKeymapManager singleton instance in TrackMateKeymapManager
tinevez
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2753205
Add a runOnClose() facility to the AbstractTrackMateModelViews
tinevez
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6662d3c
Abstract class for views based on a JFrame.
tinevez
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e8bd344
Rewrite the TrackScheme actions with the ui-behaviour framework.
tinevez
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b05eacd
Add command descriptions for TrackScheme actions.
tinevez
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1a5d981
Move the TrackMateConfigDialog to a common package.
tinevez
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39bbf47
Add pref dialog action to TrackScheme.
tinevez
committed
8660c4b

Commits on Aug 3, 2026

A GUI model class to store all info required by the full app.
tinevez
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8d0515a
A WindowManager class.
tinevez
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b13ad32
Use the new GuiModel and WindowManager in TrackMate.
tinevez
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dd551d5
Remove the unused ViewFactory framework.
tinevez
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e6408b2
Remove the unused TrackMateConfigDialog
tinevez
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15abd9f
A class to intercept user closing an ImagePlus.
tinevez
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f5e4f91
A new 64x64 TrackMate icon.
tinevez
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928731e
Set the main view apart in the WindowManager.
tinevez
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bce640e
Hook up onClose() actions on the main view.
tinevez
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b72466a
Ask for confirmation when user closes the main view of the wizard.
tinevez
committed
9a9c1e5

Commits on Aug 4, 2026

Add the mouse and key proxies to the ImagePlus canvas AND window.
tinevez
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9bf6d9d
GuiModel has fields for the preferences of the spot editor.
tinevez
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bd17af6
The main preferences dialog can configure the spot editor.
tinevez
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b60e167
Tweak the link spot behavior.
tinevez
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3cc7355
A new action to add and or link new spots.
tinevez
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959cfe4
Change the default shortcut for semi-automatic tracking.
tinevez
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d5fbe7c
Put back the default add spot action, but make it not mapped.
tinevez
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f3ea996
Add and register selectAll() commands.
tinevez
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f32c666
Semi auto tracking params is now a Configurator class.
tinevez
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c1831e0
Properly implements cancel and apply in the SpotEditToolSettingsPage.
tinevez
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002c4ff
Make the SemiAutoTrackingParams automatically de/serializes from/to JSon.
tinevez
committed
becd066

Commits on Aug 5, 2026

Use the config-ui JSon facility.
tinevez
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4e517f6
Let DisplaySettings implements Style< DisplaySettings >
tinevez
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ffabce4
Refactor the DisplaySettingsPanel
tinevez
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cb3b4d5
DisplaySettingsIO has methods to write / read specified files.
tinevez
committed
2a0603d
A SelectAndEditProfileSettingsPage for DisplaySettings.
tinevez
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aa1d049
The DisplaySettingsManager can be set to modify a specific instance.
tinevez
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01e14e4
The GuiModel has a DisplaySettingsManager,
tinevez
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eb2d182
Add the display settings config page to the preferences.
tinevez
committed
68b56cf

Commits on Aug 6, 2026

Commits on Aug 7, 2026

Depend on config-ui 0.0.1
tinevez
committed
e7c4186

Commits on Aug 8, 2026

Merge pull request #359 from trackmate-sc/displaysettings-in-settings-page
tinevez
authored
e286f8e
Fix bug in AddAndLinkSpotBehaviour.
tinevez
committed
2cafe3a
Merge pull request #357 from trackmate-sc/configurable-keys
tinevez
authored
89e3172
Add Assertj dep to test scope.
tinevez
committed
bb9e931
Make TrackModel.setVisibility() public.
tinevez
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2967c05
Make setting track name undoable.
tinevez
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9f5b933
Put calls to set track names between beingUpdate() / endUpdate()
tinevez
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4709c16
JUnit test for track name undo / redo.
tinevez
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fe1e34b
Edge case when listening to spot added and removed.
tinevez
committed
cedbcca
Fixes the old GraphTest utility.
tinevez
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5383f9b
A utility to test for TrackMate objects equality.
tinevez
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a446681
Undo / redo tests.
tinevez
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6546103
Optimize storage of undo states.
tinevez
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fe2fe86
More JUnit tests for undo / redo.
tinevez
committed
f91432b
Fix regression in undo / redo
tinevez
committed
d2f7441
Merge pull request #356 from trackmate-sc/model-undo-redo-2
tinevez
authored
a72928f
Merge pull request #355 from trackmate-sc/editor-undo-redo
tinevez
authored
b4261d2
Depend on config-ui v0.0.6
tinevez
committed
ca70b68
Merge branch 'v9' of github.com:trackmate-sc/TrackMate into v9
tinevez
committed
7a54586
Fix CI headless test failure

tinevez
and
claude
committed
a894d1c
Fix CI headless test failure
tinevez
committed
4ea440b
Default to control when we cannot get the toolkit getMenuShortcutKeyMaskEx
tinevez
committed
94a2034
Fix CI: skip GUI test in headless mode
tinevez
committed
c7f5188
Fix CI: skip GUI test in headless environment
tinevez
committed
a73b0dc

Commits on Aug 9, 2026

Commits on Aug 10, 2026

Depend on imglib2-mesh 1.2.0
tinevez
committed
70efb68
Depend on imglib2 and bdv versions defined upstream.
tinevez
committed
c99c6b5
SpotMesh returns a read-ony view of the mesh it wraps.
tinevez
committed
7eec17e
Use methods of imglib2-mesh v1.2.0 in the undo/redo stack.
tinevez
committed
c68100a
Simplify the mesh smoother tool.
tinevez
committed
f70a0a0
An abstract class for TrackMate views that are based on BVV.
tinevez
committed
1bc6372
Use the abstract BVV view class with the TrackMate BVV
tinevez
committed
68603da
The BVV view uses BigVolumeViewer rather than the BVVHandle
tinevez
committed
2f2fc60
Don't use a static instance in TrackMateKeymapManager.
tinevez
committed
2b6ca37
Integrate BVV context in the keymap config page.
tinevez
committed
d9d4313
Disable BVV button while a BVV is being launched.
tinevez
committed
d01d64f

Commits on Aug 11, 2026

Add BDV and BVV scope to key config discovery.
tinevez
committed
268e613
Add separate BVVKeymapManager for 3D view key bindings
tinevez
committed
b53b333
Add BVV keymap page to preferences dialog
tinevez
committed
331c959
Wire the BVV view to use its own keymap manager
tinevez
committed
bdd72b8
Share KeyPressedManager across windows
tinevez
committed
c001f41
A demo to reproduce the nighmare with the bvv keybindings.
tinevez
committed
bc5d960