Other Software

Image processing, reconstruction and rendering
Large scale image processing and quantification
Deep learning/Machine learning
Statistics
Data mining

Free software available to the microscopist (in alphabetical order):

Below you can find links to a selection of free software in alphabetical order available for image processing, image rendering, image analysis and data mining. If you think I have missed an important free image analysis package, please send me an email with details.

Plant Image Analysis webpage: collection of software tools for plant image analysis.

Image processing, reconstruction, stitching, tracking and rendering:

3D slicer: "open source software platform for medical image informatics, image processing, and three-dimensional visualization". Fedorov et al (2012) Magnetic Resonance Imaging 30:1323-1341.
Aivia Community: Free Aivia viewer for 2-to-5D microscopy data sets.
BioImage Suite: "an integrated image analysis software suite developed at Yale University"
BioImageXD: "free open source software for analysis, processing and 3D rendering of multi dimensional microscopy images." (I had some problems with this program but they promise on their website to improve things in the near future; definitely a program to keep an eye on).
Blender, "free and open source 3D creation suite. It supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking, video editing and 2D animation pipeline",
BlobFinder: automatic detection of dots in fluorescent data sets (Windows only). BlobFinder, a tool for fluorescence microscopy image cytometry (2009) Comput Methods Programs Biomed. 94: 58-65.
CellECT: a tool for cell analysis in 3-D confocal microscopy membrane volumes, segmentation and tracking. Linux and MacOS.
Drishti: 3D and 4D visualisation software. Can handle large datasets.
easyFRAP: Easy to use programme to assists with quantitative and qualitative analysis of FRAP data. See also: easyFRAP: an interactive, easy-to-use tool for qualitative andquantitative analysis of FRAP data (2012) Bioinformatics Application Note 28: 1800 - 1801.
Fiji: an image processing package based on ImageJ focussed on 3D reconstruction and visualization.
FluoRender: an interactive rendering tool designed especially for neurobiologists for confocal microscopy data visualization.
FrapBot: an online FRAP analysis application. Frapbot: An open-source application for FRAP data. Cytometry. DOI: 10.1002/cyto.a.23172.
FreeSurfer Software Suite: "An open source software suite for processing and analyzing (human) brain MRI images."
Fogbank: segmentation of phase contrast, bright field and fluorescence microscopy images. Matlab. Can be run as a stand alone compiled executable in Windows using Matlab MCR 9.1 (R2016b). BMC Bioinformatics (2014) 15: 431
Gimp: A photoshop-like program for "tasks as photo retouching, image composition and image authoring".
HandBrake: "a tool for converting video from nearly any format to a selection of modern, widely supported codecs". 
Image Composite Editor: "an advanced panoramic image stitcher created by the Microsoft Research Computational Photography Group".
ImagePy: ImagePy is an open source image processing framework like ImageJ but written in Python.
iTrack4U: "Automated cell tracking and analysis in phase-contrast videos". Requires Matlab, including several toolboxes.
Icy: "an open community platform for bioimage informatics" developed at Institut Pasteur.
ImageJ: A very powerful Java image processing program with plugins and macros. See also Fiji (Fiji Is Just ImageJ).
ImageTrak: "Fluorescence Image Visualization and Analysis Software", only for the MAC (not tested).
ImageSurfer: "a sophisticated 3D imaging freeware. It allows investigators to visualize and analyze multi-channel 3D and 4D (time-lapse) volumes". Deconvolution is included. (Have not tested the software but their website looks impressive). 
Imaris Viewer: a free 3D/4D microscopy image viewer for viewing raw images as well as those analyzed within Imaris.
IMOD: "set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections". Linux, Mac and Windows.
Ilastik: (Interactive Learning and Segmentation Toolkit): "ilastik is a simple, user-friendly tool for image classification and segmentation in up to three spatial and one spectral dimension". It also has a CellProfiler module (classifyPixels) to use Ilastik results to process images within CellProfiler.
Inkscape: Open Source vector graphics editor. Linux, Mac and Windows.
Irfanview: a compact FREEWARE (for non-commercial use) graphic viewer for Windows.
ITK-SNAP: software to segment structures in 3D medical images. It provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation.
Mango: "a viewer for medical research images.  It provides analysis tools and a user interface to navigate image volumes".
MicrobeTracker Suite: "MicrobeTracker Suite is a MATLAB-based software package designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them." You need MATLAB and the Image Processing toolbox to run this suite.
Microscopy Image Browser (MIB): "a high-performance Matlab-based software package for advanced image processing, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets" from the University of Helsinki.
MorphoGraphX: open source application on Linux and Windows for the visualization and advanced analysis of 4D biological datasets.
Nessys: Nuclear Envelope Segmentation System; automated identification of cell nuclei in biological images in 3D  time series.
NeuronCyto2: "a fully automatic solution for neurite length measurement and complexity analysis". The software seems to be able to handle crossed neuritis. See: Ong et al. Cytometry Part A (2016) 89A: 747-754.
NIS-Elements Viewer: Nikon's free standalone program to view image files and datasets
OpenSeadragon: "An open-source, web-based viewer for high-resolution zoomable images, implemented in pure JavaScript, for desktop and mobile."
OsiriX: image processing software dedicated to DICOM images (Mac; 32 bit version free).
PickCells: " dedicated to the analysis of multidimensional biological images. It is a stand-alone desktop application with a graphical user interface (GUI) written in Java".
Reconstruct: "Windows (Win32) application for montaging, aligning, tracing, measuring, and reconstructing objects from serial section images." (Also for light microscopy; not tested). See also: J. C. Fiala. (2005) J. Micr. 218: 52–61.
ReViMS:  a 3D volume rendering tool for light-sheet/confocal microscopy. Piccinini et al (2017) BioTechniques 63: 227-229.
SOHA: Semi-Automated Optical Heartbeat Analysis. Windows. Cammarato et al. (2015) BioTechniques 58: 77-80.
Scribus: a desktop publishing (DTP) application which include CMYK colours and ICC colour support. It is also able to create animated and interactive PDFs. Linux, Mac and Windows.
Terastitcher: A tool for fast automatic 3D-stitching of large microscopy images even when limited memory and process power is available. Bria and Lannello (2012) BMC Bioinformatics13: 316.
Vaa3D (V3D): "Vaa3D is a handy, fast, and versatile 3D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions ... ". I have not tested it yet but it looks very impressive. Linux, Mac and PC. See also: Peng et al. (2010) Nature Biotech. 28: 348-355.
VisBio: "a biological visualization tool designed for easy visualization and analysis of multidimensional image data".
VisIt: interactive parallel visualization and graphical analysis tool for viewing scientific data. Not specific for microscope images but it look powerful for and can handle large data sets.
VLC media player: ".. cross-platform multimedia player and framework that plays most multimedia files.."
Voxx: "A Volume Rendering Program for 3D Microscopy."
ZEN lite: Free Zeiss viewer for CZI files, Windows only.
YAPiC: (Yet Another Pixel Classifier) - Pixel classification in YAPiC is based on deep learning with fully convolutional neural networks. YAPiC was designed to make this kind of AI powered pixel classification simply applicable. Currently only for Linux.
XuVTools: "XuvTools is a fully automated 3D stitching software for biomedical image data, typically confocal microscopy images. XuvTools runs on Microsoft Windows XP and Vista, Linux and Apple Mac computers. It supports 32 and 64bit operating systems".

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Large scale image processing and quantification:

Bioconductor: Bioconductor is an open source software project to provide tools for the analysis and comprehension of high-throughput genomic data and is based primarily on the R programming language. The package include several image analysis and processing toolboxes and packages.
The CellCognition Project : "Development of a fast and cross-platform image analysis framework for fluorescence time-lapse microscopy in the field of bioimage informatics." The software consist of three parts:
1. CecogAnalyser: "a cross-platform standalone graphical user interface for the time-resolved analysis of single cells."
2. CellCognition: "The CellCognition framework is designed to combine object detection and supervised machine learning for classification of morphologies with time-resolved analysis by single-cell tracking. This enables measurements of progression through morphology stages and kinetic readouts at the single-cell level."
3. FlexClassifier: "The FlexClassifier is a web-based visualization tool for classifier data such as samples and corresponding features. "
Not tested but looks very impressive! See also: Held et al. (2010) Nature Methods 7:747-754;
Schmitz et al. (2010) Nature Cell Biology 12:886-893.
The CellCognition Project : "Development of a fast and cross-platform image analysis framework for fluorescence time-lapse microscopy in the field of bioimage informatics." The software consist of three parts:
1. CecogAnalyser: "a cross-platform standalone graphical user interface for the time-resolved analysis of single cells."
2. CellCognition: "The CellCognition framework is designed to combine object detection and supervised machine learning for classification of morphologies with time-resolved analysis by single-cell tracking. This enables measurements of progression through morphology stages and kinetic readouts at the single-cell level."
3. FlexClassifier: "The FlexClassifier is a web-based visualization tool for classifier data such as samples and corresponding features. "
Not tested but looks very impressive! See also: Held et al. (2010) Nature Methods 7:747-754;
Schmitz et al. (2010) Nature Cell Biology 12:886-893.
CellProfiler: "Cell image analysis software designed for biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically". Java program, so runs on Windows, Macs and Linux systems. For advanced image analysis.
CellProfiler Analyst: "data exploration software allows interactive exploration and analysis of multidimensional data, particularly data from high-throughput, image-based experiments. It also contains a supervised machine learning system which can be trained to recognize complicated and subtle phenotypes, enabling automatic scoring of millions of cells". Java program, so runs on Windows, Macs and Linux systems. Needs also access a MySQL or Oracle server.
Cytomine: "collaborative analysis of very large images and allows semi-automatic processing of large image collections via machine learning algorithms."
Fiji: an image processing package based on ImageJ focussed on 3D reconstruction and visualization.
FociCounter: a simple program for foci marking written in Python, with several options to improve the results. see also:  Jucha et al. (2010) Mutat Res 696: 16-20.
ImageJ: a very powerful Java image processing program with plugins and macros. See also Fiji (Fiji Is Just ImageJ).
NeuronIQ: "automated pipeline for quantitative, reproducible and accurate interpretation of 3D laser confocal neuron images". Part of the CBI platform developed by the Center for Biotechnology and Informatics, Methodist Hospital Research Institute, Texas. This module needs Matlab to run.
Orbit: "Orbit Image Analysis is a free open source software with the focus to quantify big images like whole slide scans... Sophisticated image analysis algorithms incl. tissue quantification using machine learning, object segmentation and classification are build in."
PhenoRipper: Image analysis not on segmentation but by intensities in blocks. Has a powerful explorer to browse and visualise the analysis results. Rajaram et al. (2012) Nature Methods 9: 635-637.
QuPath: open source software for Quantitative Pathology. Bankhead et al. (2017) Sci. Rep 7: 16878.
TANGO: Tools for Analysis of Nuclear Genome Organization. "TANGO is a coherent framework allowing biologists to perform the complete analysis process of 3D fluorescence images by combining two environments: ImageJ1 for image processing and quantitative analysis and R2 for statistical processing of measurement results", Ollion et al. (2013) Bioinformatics 29: 1840-1841.

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Deep learning/machine learning:

The CellCognition Project : "Development of a fast and cross-platform image analysis framework for fluorescence time-lapse microscopy in the field of bioimage informatics." The software consist of three parts:
1. CecogAnalyser: "a cross-platform standalone graphical user interface for the time-resolved analysis of single cells."
2. CellCognition: "The CellCognition framework is designed to combine object detection and supervised machine learning for classification of morphologies with time-resolved analysis by single-cell tracking. This enables measurements of progression through morphology stages and kinetic readouts at the single-cell level."
3. FlexClassifier: "The FlexClassifier is a web-based visualization tool for classifier data such as samples and corresponding features. "
Not tested but looks very impressive! See also: Held et al. (2010) Nature Methods 7:747-754;
Schmitz et al. (2010) Nature Cell Biology 12:886-893.
Cellpose: cellpose is an anatomical segmentation algorithm that often works out of the box. See also Stringer et al. (2020) bioRxiv preprint doi: https://doi.org/10.1101/2020.02.02.931238
CellProfiler Analyst: "data exploration software allows interactive exploration and analysis of multidimensional data, particularly data from high-throughput, image-based experiments. It also contains a supervised machine learning system which can be trained to recognize complicated and subtle phenotypes, enabling automatic scoring of millions of cells". Java program, so runs on Windows, Macs and Linux systems. Needs also access a MySQL or Oracle server.
Cytomine: "collaborative analysis of very large images and allows semi-automatic processing of large image collections via machine learning algorithms."
DeepLabCut Model Zoo: several trained models for animal pose estimation.
Orbit: "Orbit Image Analysis is a free open source software with the focus to quantify big images like whole slide scans... Sophisticated image analysis algorithms incl. tissue quantification using machine learning, object segmentation and classification are build in."
QuPath: open source software for Quantitative Pathology. Bankhead et al. (2017) Sci. Rep 7: 16878.
YAPiC: (Yet Another Pixel Classifier) - Pixel classification in YAPiC is based on deep learning with fully convolutional neural networks. YAPiC was designed to make this kind of AI powered pixel classification simply applicable. Currently only for Linux.
Yolo: real time object detection 
ZeroCostDL4Mic: exploiting Google Colab to develop a free and open-source toolbox for Deep-Learning in microscopy using a collection of self-explanatory Jupyter Notebooks.

Statistics:

Bio7: ImageJ integrated in an ecological modelling environment including Statistical analysis (R).
R: "R is a language and environment for statistical computing and graphics".
SOFA: Statistics Open For All. "SOFA is a user-friendly statistics, analysis, & reporting program. It is free, with an emphasis on ease of use, learn as you go, and beautiful output."

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Data mining:

KEEL: "software tool to assess evolutionary algorithms for Data Mining problems including regression, classification, clustering, pattern mining and so on......  KEEL contains a big collection of classical knowledge extraction algorithms, preprocessing techniques, Computational Intelligence based learning algorithms, including evolutionary rule learning algorithms based on different approaches (Pittsburgh, Michigan and IRL, ...), and hybrid models such as genetic fuzzy systems, evolutionary neural networks, etc." Java program, so runs on Windows, Macs and Linux systems.
KNIME: "a modular data exploration platform that enables the user to visually create data flows, selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models". Available for Windows and Linux.
Orange: "Orange is a component-based data mining software. It includes a range of preprocessing, modelling and data exploration techniques. It is based on C++ components, that are accessed either directly (not very common), through Python scripts (easier and better), or through GUI objects called Orange Widgets." Seems user friendly. Download includes all extensions and Python. Available for Windows, Linux and Macs.
RapidMiner: "The main product of Rapid-I is the data analysis solution RapidMiner, the world-leading open-source system for knowledge discovery and data mining." Seems very useful and relative easy in use but I had problems with some menus being unreadable when testing this package. There is Windows version and a Java version for any platform.
Rattle: "A Graphical User Interface for Data Mining using R." 
TANAGRA: " TANAGRA is a free DATA MINING software for academic and research purposes. It proposes several data mining methods from exploratory data analysis, statistical learning, machine learning and databases area. " Windows version only.

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