Pinned Repositories
fiji
A "batteries-included" distribution of ImageJ :battery:
bioformats
Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment (particularly UW-Madison LOCI and Glencoe Software). Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
imagej-legacy
ImageJ+ImageJ2 compatibility layer
ITK
imagej-matlab
MATLAB integration with ImageJ data structures and runtime.
imagej-ops
ImageJ Ops: "Write once, run anywhere" image processing
imagej2
Open scientific N-dimensional image processing :microscope: :sparkler:
tutorials
ImageJ2 programming examples
scifio
SCientific Image Format Input & Output: a flexible, extensible framework for image I/O. *EXPERIMENTAL* All API is subject to change, so depend at your own risk! See also @openmicroscopy/bioformats.
hinerm's Repositories
hinerm/imagej-legacy
ImageJ+ImageJ2 compatibility layer
hinerm/cache-tests
test sandbox for GitHub actions cache mechanisms
hinerm/caterpillars
Dynamic caterpillar documentation
hinerm/CellProfiler
An open-source application for biological image analysis
hinerm/CellProfiler-plugins
Community-contributed and experimental CellProfiler modules.
hinerm/core
hinerm/cp-proc
Process experimentation
hinerm/DeformingMesh3D-plugin
An imagej/fiji plugin for interactive segmentation of 3D
hinerm/dotfiles
My configuration files.
hinerm/fiji-builds
Downloadable Fiji bundles
hinerm/FijiRelax
FijiRelax: 3D+t multi-echo spin-echo sequences MRI analysis
hinerm/ij1-builds
Continuous integration machinery for ImageJ 1.x
hinerm/ImageJ
Public domain software for processing and analyzing scientific images – a.k.a. ImageJ 1.x
hinerm/imagej-launcher
The ImageJ native launcher
hinerm/imglib2-trainable-segmentation
hinerm/imglyb
Connecting Java/ImgLib2 + Python/NumPy
hinerm/incubator
Where development happens and stuff breaks 🛠️
hinerm/JEX
Java-based software and GUI to automatically manage/database large numbers of files (e.g., images) in a transparent file structure and perform batch processing with standard tools (ImageJ, R, Octave, Weka).
hinerm/jfilament
Active countour based segmentation. FIJI plugin.
hinerm/jgo
Launch Java code from the CLI, installation-free. ☕
hinerm/jitk-tps
A java port of the ITK thin plate spline implementation.
hinerm/MorphoLibJ
Collection of mathematical morphology methods and plugins for ImageJ
hinerm/MTrack
Microtubule tracker@V Kapoor
hinerm/multiview-reconstruction
Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data
hinerm/multiview-simulation
Code for simulating a multi-view acquisition including attenuation, convolution, reduced sampling and poission noise
hinerm/prokaryote
CellProfiler’s Java dependencies
hinerm/pyimagej
Use ImageJ from Python
hinerm/scyjava
⚡ Supercharged Java access from Python ⚡
hinerm/TrackMate-extras
Some extra modules for TrackMate
hinerm/TrackMate-TrackAnalysis
Basic track analysis, plugged as TrackMate modules.