The framework for quantification of neuronal anatomy
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Oct 12, 2026 - Java
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imagej2
Here are 23 public repositories matching this topic...
🔬🍸 Home of the ImageJ BAR: A collection of Broadly Applicable Routines for ImageJ
ruby python java groovy clojure imagej imagej2 scripts-collection scientific-workflows image-analysis microscopy jython beanshell ijm
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Jun 3, 2022 - Java
The Cx3D modeling framework in SciView and SNT
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Apr 3, 2024 - Java
Cell segmentation of multi-channel images
imagej2 batch cells nuclei bio-formats multi-channel macro ihc cell-segmentation membrane polaris vectra immunohistochemistry pixel-classifier akoya-biosciences ionpath cytoplasm cell-matrix trainable-weka-segmentation mibiscope
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May 8, 2023 - ImageJ Macro
A collection of scripts related to Micro-Manager.
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Mar 2, 2019 - Shell
Open-source image alignment and brain atlas registration for Fiji / ImageJ2. Review mouse brain microscopy against Allen CCFv3, select anatomical ROIs, and export crops and masks. Supports resumable batch review.
java open-source imagej imagej2 fiji neuroscience roi microscopy image-registration allen-brain-atlas histology image-alignment brain-atlas bioimage-analysis immunofluorescence roi-analysis atlas-registration ccfv3
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Sep 11, 2026 - Java
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Mar 7, 2022 - Java
IHC scoring of multi-channel images
imagej2 scoring batch bio-formats multi-channel macro dab ihc polaris immunofluorescence vectra staining immunohistochemistry akoya-biosciences ionpath hematoxylin mibiscope
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Apr 26, 2023 - ImageJ Macro
☕ 🐍 🔬 Package for processing metadata from various light-microscopy related data formats.
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Jan 22, 2026 - Python
ImageJ plugin for handling NDPI files.
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Aug 20, 2025 - Java
Mageek is an ImageJ Java plugin to batch process microscope images
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Mar 16, 2022 - Java
An Imagej Plugin for Large Scale Image Data Augmentation
deep-learning imagej imagej2 fiji image-processing java-8 imagej-plugins data-augmentation image-augmentation fiji-plugin image-augmentor image-augmentation-preprocessing image-augmentations
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Jan 30, 2024 - Java
A Spark-interface for the io.scif and other libraries to take advantage of the ImageJ2 ecosystem.
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Apr 26, 2024 - Scala
Prairie 2-Photon Microscopy Data Manager for recursive batch processing ans analysis with Fiji
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Jun 18, 2021 - ImageJ Macro
ImageJ Fiji plugin containing 12 FR-IQA measures for grayscale images.
imagej2 imagej-plugins image-quality-assessment full-reference-iqa full-reference-image-quality-assessment
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Aug 17, 2025 - Java
Write SciJava scripts in Jupyter notebook!
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Aug 21, 2018 - Java
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