Qiqi Lu Southern Medical University

Softwares for Microscopy Images

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.