Connect Napari with FIJI/ImageJ
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Updated
Aug 7, 2024 - 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.
Connect Napari with FIJI/ImageJ
Python script to facilitate the processing of data obtained with the AnalyzeSkeleton tool from Fiji/ImageJ
Example scripts and macro for scripting with the ACQUIFER Java API
Fiji plugin for object(s) detection using template(s) matching
🔧 📝 ☕ 🔬 Scripts for Fiji provided by the Imaging Core Facility, Biozentrum, University of Basel
Scripts for executing Fiji plugin BoneJ in headless mode in Python to compute bone microstructure metrics
Measures the integral radial density of a fluorescent signal in a nucleus of any shape
ANDA: An open-source tool for automated image analysis of in vitro neuronal cells
Fiji/ImageJ plugin to help measuring linear distances.
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.
A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification
MRI ImageJ related python (jython) module.
A collection of scripts to automate the steps for the quantification of vascular-like structures in 3D using Amira, Fiji/ImageJ and WinFiber3D.
Plugins for ImageJ/FIJI