DM3D

ThreeD image segmentation algorithm, for roundish cells.

The latest documentation can be found at:

Roadmap 1.0 Draft

As of version 0.8.0 these features have been added. There are some details that need to be worked out. Especially documentation.

This is the start of a draft for a 1.0 release version. Right now I have quite a few components that are nearly ready but need to be added. The two major features that I want included in a 1.0 release.

installation

The easiest way to install this plugin is through the Fiji update site.

Run Fiji, choose the menu "help", select "update..." after updating there will be a dialog that has "Manage Update Sites".

https://sites.imagej.net/Odinsbane

Once the site has been added, updating fiji should cause it to download and install the deforming mesh plugin which can be found in "plugins"->"PL_Mesh3D"->"Deforming Mesh 3D", and JFilament will also be installed.

Documentation

DM3D Github pages

This includes guides for using the plugin, and javadoc for using the plugin via scripting.

Changes

0.9.8

Changed volume calculation technique.
Added a way to create training labels from a labelled image.

0.9.7

improved slice view synchronization
added sculpt/select items to slice view
Limited title length
Changed the way errors are displayed

0.9.6

updated scijava pom
added flatlaf to pom
created a way to substitute image data
added a way to remove all tracking information
added a remote prediction class (experimental)
removed cursor radius controls, added javascript portal
improved display for hidpi developing with flatlaf for consistency
Added run file to javascript console
Added faq to help menu.

0.9.4

Improved autotracking accessiblity.
- linkPossibleTrack() to link the selected track.
- autotrackAvailableTracks() attempts to link all available in the first frame with the second frame.
Import from open image has been created, for loading meshes from different image geometries.
Connection remeshing calculates the expected number of connections differently/better.
Orient the furrow from the 3D canvas.
Flip the furrow.
BUG FIX: empty tracks get removed from the manager. 0.9.2
3D viewer has been improved to handle viewing small sections of large images. 0.9.1
BUG FIX track manager selects correct mesh. 0.9.0
Selected mesh is now updated in track manager.
Exposing averaged intensity vs time plot
exposed frame to frame displacement simple auto tracker.
Updated mesh file reading to include progress and range checking.

0.8.0

Select channel from main display.
Added 3D sculpting - feature preview version.
mesh track manager and undo/redo follow the state of the ActionManager.
deformAllMeshes has a limit, can be used in a script.
restartOffScreenCanvas javascript function to address bug in offscreen canvas.
scaled units are indicated for connection remesh.
histogram display improved.
3D preview removed for now.
Meshes can have transparency.

0.7.0

Creating Binary images algorithm improvement.
Visualization improvements.

0.6.0

Feature preview modifier and limited controls to the furrow panel. Debugging for next release.
created 2d svg/image view and exposed through javascript
added normals to the data object, that need to be updated.
light tracks the display.
objects are lit by a single directional light, and an ambient light.
lighting can be adjusted in the mesh viewer to find better lighting settings.
moved the ring controller to be in the controlframe
exposed mesh sculpting via the furrow3d view input
BUG FIX slice view 3d scrolling
made the modification cursor size adjustable.
ui overhaul
track manager has select all/ select all before/ and select all after
track manager modifies names to avoid duplicates.

0.5.0

moved initializer to a new frame.
Created a non-3d mode
BUG FIX names can break mesh loading.
BUG FIX track manager changes show surface.
Split mesh and deform partial available from java script.
Some linear plots.
Moved manage tracks to a tabbed pane.
Improved non-3d version to run program for running over x11 forwarded.
steric mesh uses shorted distance along normal.
improved redo/undo
"SegmentationController.selectTrack" was broken.
Bug fix: BinaryInterceptible was off by 1 for z axis.
Furrow3D shows the texture.
Furrow input panel is changing design.
Histogram input is smaller and adjustabble.
show/hide furrow.
Meshes are now selectable from the furrow screen.
Worked on the import meshes. Created 4 types of import. Checked each on. do and undo seemed to work.
Removed a bug where removing a track would empty all of it's meshes, breaking undo.
Added labels to the histogram control.
Implemented the curvature smoothing algorithm. Not sure if it does anything.
Channels now sync to the frame when they're added.
BinaryInterceptible considers edge of image points as edges.
Added limited transparency control
Added mesh projections to the Furrow tab.
Restructuring the furrow tab layout.
Remove the field 'original_stack'
Adding a non-energy option.
Added channel select when selecting an open image plus.

0.3.9

Added connection remesher to control panel.
Multi channel support
- Display multiple volumes as channels
- Select a single channel from a multi-channel image
Steric Energy improvements
Exposed auto-detect meshes through javascript

0.3.8

Contrast preview dialog matches the clamped values.
Removed the normalizer weight from controls, added steric neighbors.
Exposed connection remesher in javascript with min/max lengths.
Contrast adjustment for displayed channels.

0.3.7

Added key command actions to 3D display.
Added help screen to hud to display key commands.
Added mesh export options for wire-frame and shell meshes.
Swing javascript terminal has a shortcut execution mode.
Contrast adjustment tool.
Selecting open image returns to the current frame for swapping energies.
Improved 3D volume data handling, now is a DataObject.
Created a 3D surface for volume textures.
Improved 3D geometry display performance.
python meshes have a reader and writer.
Bug fix: color selection could cause infinite loop.
Connected components refactoring.
Connection based remeshing *
Manual Mesh editing *
Forces can be displayed as vectors *
VolumeDataObject is accessible through MeshFrame3D api for displaying multi-channels. *

only available through javascript.

0.3.6

javascript available actions improved.
surface plots available through javascript interface.
steric forces improved.
clear mesh from current frame.
transformations to look at plane.

0.3.5

Initial window size checks monitor size and attempts to be <=80%
Mesh initialization zoom keeps cursor location the same.
ctrl + drag to move mesh initialization views.
3 and 1 panel views during initialization
Create and show a binary representation of currently selected mesh.
stl writing improved.
Added a cursor to the initialization window.
BUG FIX: load meshes now finishes when canceled.
BUG FIX: restart meshes, undoable.
load/save parameters
Initialization sliders are finer controlled.
Can now switch image by selecting open image.

0.3.4

status panel/mesh color display
ctrl z /ctrl-shift z undo/redo respectively
js terminal has suggestions and completions
track backwards
frame number displays 1 off of index. (looks like imagej's 1 index scheme)
exports to ply file.
Mesh track manager for tracking arranging meshes through time.
user preferences are saved

Reference

Chapter 19 - An active contour ImageJ plugin to monitor daughter cell size in 3D during cytokinesis

MB Smith, A Chaigne, EK Paluch