JIPipe
JIPipe is a visual programming language for ImageJ that allows you to create macros without any programming by just creating a flowchart.
Cellpose
Cellpose is a generalist algorithm for cell and nucleus segmentation (v1.0) that can be optimized for your own data (v2.0) and perform image restoration (v3.0).
ModularImageAnalysis (MIA)
MIA is a Fiji plugin providing a modular framework for assembling image and object analysis workflows.
napari
Napari is a Python library for n-dimensional image visualisation, annotation, and analysis.
Napari plugins are just Python packages.
napari-imagej
napari-imagej is a layer on top of PyImageJ (i.e., a napari plug-in), automating data conversions and enabling access to ImageJ funcitonality within one unified napari interface.
Operation systems: Linux, macOS, Windows
deepImageJ
DeepImageJ is a user-friendly plugin that enables the use of a variety of pre-trained neural networks in ImageJ and Fiji.
It gives access to the largest bioimage repository of pre-trained deep learning models (BioImage Model Zoo)
BioImage.IO
BioImage.IO or BioImage Model Zoo is an repository for sharing AI models, datasets and tools for bioimage analysis.
CSBDeep
CSBDeep is a deep learning toolbox for microscopy image restoration and analysis.
ZS-DeconvNet Fiji plugin
ZS-DeconvNet Fiji plugin is a Java-based plugin for ZS-DeconvNet, which enables one-click training and inference of ZS-DeconvNet.
The ZS-DeconvNet Fiji plugin was developed based on TensorFlow-Java 1.15.0, which is compatible with CUDA version of 10.1 and cuDNN version of 7.5.1.
For the model developed using Pytorch and Java, DeepJavaLibrary may be a choice.
PyImageJ
PyImageJ is a robust solution for Python-based ImageJ access, including its data structures and plug-ins.
PyImageJ is a libaray for programmers, requiresing expplicit conversion of Python data structures such as Numpy images into equicalent Java before they can be passed to ImageJ routines.
ZeroCostDL4Mic
ZeroCostDL4Mic is a toolbox for the training and implementation of common Deep Learning approaches to microscopy imaging and a collection of self-explanatory Jupyter Notebooks for Google Colab.. It exploits the ease of use and access to GPU provided by Google Colab.
DL4MicEverywhere
DL4MicEverywhere is an open-source platform that aims to make deep learning more accessible for bioimage analysis. It builds on the previous ZeroCostDL4Mic platform and advances it further to allow more flexible training and deployment of deep learning models across diverse computational environments.
ImJoy
ImJoy’s core is a severless pregressive web application offering a fast and reliable user experience across all mainstream platforms, including laptops and mobile devices.
ImJoy’s functionalities are provided by independently operating plugins (written in different languages) that can be organized into workflows.
ilastik
ilastik is an interactive learning and segmentation toolkit.
Icy
Icy is an open community platform for bioimage informatics.
Language: Java
NIH Image
NIH Image is the precursor to ImageJ.
ImageJ
ImageJ is public domain software for processing and analyzing scientific images, with many derivatives and variants, including ImageJ2, Fiji, and others.
Language: Java
ImageJ2
ImageJ2 is a rewrite of ImageJ for multidimensional image data, with a focus on scientific imaging.
Language: Java
Fiji
Fiji is an image processing package—a “batteries-included” distribution of ImageJ2, bundling a lot of plugins which facilitate scientific image analysis.
Language: Java
BioImageXD
BioImageXD is a free open source software package for analyzing, processing and visualizing multi-dimensional microscopy images.
Language: C++ or Python
CellProfiler
CellProfiler is a free open-source cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
Language: Python
QuPath
QuPath is an open source software for bioimage analysis and can be esily integration with other tools, including ImageJ.
Language: Java
KNIME
KNIME offers a complete platform for end-to-end data science, from creating analytic models, to deploying them and sharing insights within the organization, through to data apps and services.
StarDist
StarDist is an Python implementation of star-convex object detection for 2D and 3D images.
Language: Python
BiaPy
BiaPy is an open source Python library that provides deep-learning workflows for a large variety of bioimage analysis tasks, including 2D and 3D semantic sgmentation, instance segmentation , object detection, image denoising, single image super-resolution, self-supervised learning, image classification and image to image translation.
BioImage Suite
BioImage Suite is a web-based medical image analysis software with image processing, image registration and visulization capabilities.
Vaa3D
Vaa3D (3D visualization-assisted analysis) is an open-source software suite for multi-dimensional data visualization and analysis.
VisBio
VisBio is a biological visualization tool designed for easy visualization and analysis of multidimensional image data. It displays data with VisAD and is bundled with ImageJ.
Language: Java
VisAD
VisAD is a Java component library for interactive and collaborative visualization and analysis of numerical data.