tischi/segmentation-annotator

Segmentation annotator

Segmentation Annotator is a Fiji plugin for the inspection and annotation of segmented images.

Social media

• Forum thread

Demonstration movies

Explore

Annotate

Render Objects in 3D

Install

1. Please install Fiji onto your computer.
2. Start Fiji and add the Update Site SegmentationAnnotator like this:
   • [ Help > Update.. ]
   • [ Manage update sites ]
     • SegmentationAnnotator
   • [ Close ]
3. Restart Fiji

Quick start

After installation (see above). You can run below ImageJ macros to launch the application:

• Minimal 2D segmented image exploration
• A bit larger 3D segmented image exploration

Run

After installation the following entries are available in the ImageJ menu:

• [ Plugins > Segmentation > Annotator > Open Dataset from Table... ]
  • Experimental (Do not use yet).
• [ Plugins > Segmentation > Annotator > Open Intensity and Label Mask Image... ]
  • Allows you to select an intensity image and label mask image from the currently open images.
  • It will automatically compute few basic features of the segmented objects.
• [ Plugins > Segmentation > Annotator > Open Intensity and Label Mask Image and MorpholibJ Results Table... ]
  • As the command above but you can in addition select an object measurements table generated with MorpholibJ.

Use

• Mouse: Right click: Shows a context menu through with most functionality can be accessed.
• Mouse: Ctrl + Left-Click: Selects/Deselects the image segment at the location of the mouse pointer.