ImageJ scripts for stereology and morphometry
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Updated
Jul 19, 2017 - Python
ImageJ is an open source Java image processing program inspired by NIH Image.
It runs on any computer with a Java 1.8 or later virtual machine.
Downloadable distributions are available for Windows, Mac OS X and Linux.
ImageJ has a strong, established user base, with thousands of plugins and macros for performing a wide variety of tasks.
Fiji is a "batteries-included" distribution of ImageJ, bundling many plugins which facilitate scientific image analysis.
ImageJ scripts for stereology and morphometry
ImageJ scripts for analyzing nuclei intensity and overlap in brain sections
A collection of handy FIJI macros for image processing.
A repository containing ImageJ macros for the Snyder Lab
Plugins for ImageJ/FIJI
A collection of scripts to automate the steps for the quantification of vascular-like structures in 3D using Amira, Fiji/ImageJ and WinFiber3D.
MRI ImageJ related python (jython) module.
A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification
FijiTools2020 is a collection of tools designed for use in ImageJ/Fiji. The code was written for the analysis of microscopy images in the lab of Mikael Sellin, Uppsala University. Some of the scripts are meant to work in conjunction with a separately performed Trackmate analysis.
Fiji/ImageJ plugin to help measuring linear distances.
Connect Napari with FIJI/ImageJ
ANDA: An open-source tool for automated image analysis of in vitro neuronal cells
Measures the integral radial density of a fluorescent signal in a nucleus of any shape
Scripts for executing Fiji plugin BoneJ in headless mode in Python to compute bone microstructure metrics