Similar Projects

This is a growing collection of open source biological image stack analysis software similar to flika. If you think we’ve missed something, please contact us. This list is grouped by programming language.



CaImAn is a computational toolbox for large scale Calcium Imaging Analysis of neurons, including movie handling, motion correction, source extraction, spike deconvolution and result visualization. It is maintained by the Flatiron institute, a divison of the Simons Foundation.


CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

Mesoscale Brain Explorer

A program for analysis of widefield optical brain imaging.


SIMA (Sequential IMage Analysis) is an Open Source package for analysis of time-series imaging data arising from fluorescence microscopy. The functionality of this package includes:

  • correction of motion artifacts
  • segmentation of imaging fields into regions of interest (ROIs)
  • extraction of dynamic signals from ROIs


BioImageXD is a free open source software package for analyzing, processing and visualizing multi-dimensional microscopy images. It’s a collaborative project, designed and developed by microscopists, cell biologists and software engineers from the Universities of Jyväskylä and Turku in Finland, Max Planck Institute CBG in Dresden, Germany and collaborators worldwide. BioImageXD was published in the July 2012 issue of Nature Methods.


ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection. Most analysis operations are performed lazily, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode. Using it requires no experience in image processing.

CHIPS (not yet published)

CHIPS: Cellular and Hemodynamic Image Processing Suite


ImageJ (aka FIJI)

Developed at the NIH by Wayne Rasband, ImageJ is probably the most popular image analysis software for biologists. FIJI is an easily installable distribution of ImageJ that includes many popular plugins.


Endrov is a multi-purpose image analysis program. It is written indepedently and designed to address many of the shortcomings of other free software and many commercial packages. Endrov has been published in Nature Methods.


GemIdent is an interactive program that identifies regions of interest in images. It is specifically designed for color segmentation in images with few colors, where the objects of interest look alike with small variation. For example, oranges in a tree (see quick demo and cells in microscopic images (see histological demo).


C, C++


VIAS stands for Volume Integration and Alignment System. It is designed to allow multiple stacks of tiled optical sections obtained from Laser Scanning Microscopy to be integrated into a single volumetric dataset. Currently only 8 and 16 bit grayscale images are supported.


The FARSIGHT framework is built around a “divide and conquer” approach to the image segmentation problem, taking advantage of the molecular specificity of fluorescence microscopy (the F in FARSIGHT stands for fluorescence). Specifically, it is very practical now to label each of the bio-molecules of interest using highly specific fluorescent labels and good specimen preparation protocols. Aided by spectral imaging hardware and spectral unmixing software, each of the biological entities of interest can be imaged separately into non-overlapping channels with negligible cross talk. Mixed channels containing more than one object type are still possible, but increasingly rare. FARSIGHT is intended to be used within this realm.


OME Remote Objects (OMERO) is a modern client-server software platform for visualizing, managing, and annotating scientific image data. OMERO lets you import and archive your images, annotate and tag them, record your experimental protocols, and export images in a number of formats. It also allows you to collaborate with colleagues anywhere in the world by creating user groups with different permission levels. OMERO consists of a Java server, several Java client applications, as well as Python and C++ bindings and a Django-based web application.