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Fiji is Just ImageJ: an ImageJ distribution with many plugins bundled along, including TrakEM2. The whole of Fiji software repository is under version control with git.
What I use Fiji for:
I have started also a series of ImageJ Programming Tutorials and a tutorial on scripting Fiji with jython (python for the JVM).
What is TrakEM2: an ImageJ plugin for 3D modeling, image annotation, automatic montage-making, image alignment, and everything I need for neuroscience in Drosophila. The program can handle arbitrarily large image datasets (my largest one so far is 350 Gb). There is a manual and a couple of snapshots of TrakEM2 in action.
My daily use of TrakEM2:
- Assembling montages from TEM image acquisition of serial sections.
- Registering TEM serial sections
- Segmenting neurites from TEM images, generating 3D meshes and visualizing them in the built-in 3D-accelerated viewer, and exporting the 3D meshes for rendering with ray-tracing in Blender.
- Annotating TEM images with floating text labels.
- Sketching neurites and cell bodies in confocal microscopy stacks.
All the above, of course, within the excellent image processing environment provided for free by ImageJ.
CATMAID is the Collaborative Annotation Toolkit for Massive Amounts of Image Data. The source code is under version control with git and lives in a github repository. We use CATMAID to deploy enormous datasets via the web, in an interface inspired by Google Maps.
Data sets deployed with CATMAID:
Last updated: 2016-02-17 09:36 New York time. Copyright Albert Cardona.