Automated

The Arabidopsis Seedlings Tool allows to analyze the germination and seedling growth of Arabidopsis (Arabidopsis thaliana) in liquid culture. It measures the surface of green pixels per well in images containing multiple wells. It can be run in batch mode on a series of images. It writes a spreadsheet file with the measured area per well and saves a control image showing the green surface that has been detected per well. 

See http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Arabidopsis_Seedlings_Tool

Test images can be found here.

IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files.

Included are two programs with graphical interface: 3dmod, for displaying and segmenting 2D images and 3D volumes; etomo, for reconstructing tomographic volumes from tilt series of images.

Processing can be distributed on multiple cores and executed in batch mode.

MATLAB is famous, so this page is only for being the landing page for components and workflows.

Acquiarium is for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation. It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.

Columbus is a combination of an image database (based on Omero, OME) and an image analysis engine based on Acapella (PerkinElmer). It is dedicated to cell culture based high content screening data and is used via a web interface. It provides a set importers for automated microscopes such as Yokogawa CellVoyager, PerkinElmer Operetta, PerkinElmer Opera and data in Metamorph format. After login, Images can be explored in a standard web browser by clicking on a well plate view. Image analysis workflows can be developed by combining modules like "find nuclei", "find cytoplasm", "find spots" for object detection. Objects can have a hierarchical structure, e.g. spot objects can be part of a cell object. The approach of workflow design is similar to the freeware cell profiler, but more restricted (less functions and less parameters to tweak) and easier to use. Mutliple intensity- and shape based features can be calculated from detected objects (e.g. texture: haralick, Garbor, SER). Objects can be classified by these features by using hard thresholds or by supervised machine learning. Analysis workflows and results are stored in the database and can be exprted as csv tables for secondary analysis. Simple secondary analysis workflows can be also applied in Columbus directly. Results can be visualized as heatmaps on the plate view. The HCS statistics software Genedata Screener Assay Analyzer can be directly connected to the database.

Slicer, or 3D Slicer, is a free, open source software package for visualization and image analysis. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X.

An ImageJ macro for correcting frame drift occurred during image acquisition.

It often happens that you have an image sequence that shows problematic drifting of image frame and at the same time you have some landmarks that could be used for correcting the drift. This ImageJ macro allows you to Manually track the landmark using ImageJ Manual Tracking Plugin. Using the coordinates recorded in the Result window, each frame is shifted back so that the landmark stays in a single place.

BioImage Analysis Tool for all! Also check out ImageJ2

u-track is a multiple-particle tracking Matlab software that is designed to (1) track dense particle fields, (2) close gaps in particle trajectories resulting from detection failure, and (3) capture particle merging and splitting events resulting from occlusion or genuine aggregation and dissociation events. Its core is based on formulating correspondence problems as linear assignment problems and searching for a globally optimal solution.

Data can be read using bio-format and interfaced with OMero data base.

It comes as a standalone software, but can be used as a library, which is according to the authors the most widely used version of it.

• Version 2.2 adds parallel processing functionality for multi-movie datasets when using the GUI.
• Version 2.1 enables the analysis of movies stored on an OMERO server
• Version 2.0 includes two new tracking applications: microtubule plus-end tracking (previously distributed as plusTipTracker) and nuclei tracking
• A third optional processing step has been added to the analysis workflow, track analysis, with two methods: motion analysis and microtubule plus-end classification

For more information, please see Jaqaman et al., Nature Methods 5, pp. 695-702 (2008). Besides basic particle tracking, the software supports the features described in Applegate et al. J. Struct. Biol. 176(2):168-84. 2011 for tracking microtubule plus end markers; and in Ng et al. J. Cell Biol. 199(3):545-63. 2012 for tracking fluorescently-labeled cell nuclei.

ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis.

Developed through extreme programming methodologies, ITK employs leading-edge algorithms for registering and segmenting multidimensional data. It is widely used and contributed in the medical imaging field.

Strengths

Highly optimized C++, well commented Consistently updated (new) algorithms many tools and softwares are built upon it connected with VTK Insight Journal (open code and sample data) Extensive list of examples & tutorials

Limitations

yet detached from the bioimage analysis world hard to use for end users without development skills

Schnitzcells is a MATLAB based software that allows for quantitative analysis of fluorescent time-lapse movies of living cells. The software package is developed most specifically for bacteria and has been instrumental in analyzing E.coli and B. subtilis movies. The software contains functions that segment cells (based on either fluorescence or phase images),tracks cells in a frame-to-frame manner,build lineage trees and quantitatively extracts fluorescence.

Strength: tools for manually editing segmentation and lineage, well documented, free matlab source code, sample data

Limitations: no support, changes need to be done directly in the matlab code

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.

ilastik (the image learning, analysis, and segmentation toolkit) provides non-experts with a menu of pre-built image analysis workflows. ilastik handles data of up to five dimensions (time, 3D space, and spectral dimension). Its workflows provide an interactive experience to give the user immediate feedback on the quality of the results yielded by her chosen parameters and/or labelings.

The most commonly used workflow is pixel classification, which requires very little parameter tuning and instead offers a machine learning technique for segmenting an image based on local image features computed for each pixel.

Other workflows include:

Object classification: Similar to pixel classification, but classifies previously segmented objects by object characteristics in a subsequent step

Autocontext: This workflow improves the pixel classification workflow by running it in multiple stages and showing each pixel the results of the previous stage.

Carving: Semi-automated segmentation of 3D objects (e.g. neurons) based on user-provided seeds

Manual Tracking: Semi-automated cell tracking of 2D+time or 3D+time images based on manual annotations

Automated tracking: Fully-automated cell tracking of 2D+time or 3D+time images with some parameter tuning

Density Counting: Learned cell population counting based on interactively provided user annotation

Strengths: interactive, simple interface (for non-experts), few parameters, larger-than-RAM data, multi-dimensional data (time, 3D space, channel), headless operation, batch mode, parallelized computation, open source

Weaknesses: Pre-built workflows (not reconfigurable), no plugin system, visualization sometimes buggy, must import 3D data to HDF5, tracking requires an external CPLEX installation

Supported Formats: hdf5, tiff, jpeg, png, bmp, pnm, gif, hdr, exr, sif

Imaris is a software for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy images. It performs interactive volume rendering that lets users freely navigate even very large datasets (hundreds of GB). It performs both manual and automated detection and tracking of biological “objects” such as cells, nuclei, vesicles, neurons, and many more. ImarisSpots for example is a tool to detect “spherical objects” and track them in time series. Besides the automated detection it gives the user the ability to manually delete and place new spots in 3D space. ImarisCell is a tool to detect nuclei, cell boundaries and vesicles and track these through time. ImarisFilament is a module that lets users trace neurons and detect spines. For any detected object Imaris computes a large set of statistics values such as volume, surface area, maximum intensity of first channel, number of vesicles per cell etc. These values can be exported to Excel and statistics software packages. The measurements can also be analyzed directly within ImarisVantage which is a statistics tool that provides the link back to the 3D objects and the original image data. Strengths: - good visualization - user friendly interface - reads most microscopy file formats - image analysis workflows are very easy to apply - interactive editing of objects to correct errors during automatic detection - large data visualization (hundreds of GB)

Reproducing an experiment doesn’t stop at the bench when images are concerned. Icy is an open source bioimaging software package that aims to provide a framework for authors to share, and others to reproduce, research once the sample hits the microscope. Icy was released in April 2011 and is being developed at the Quantitative Image Analysis Unit at the Pasteur Institute in France by Jean-Christophe Olivo-Marin and his team. The goal is to provide standardized software architecture, with a visual programming framework and online repository of plugins and protocols, brought together with sophisticated content-management and communication systems for such extended reproducible research. Icy provides intuitive user interfaces for graphical protocol development for image acquisition, analysis and storage that are easy to use for biologists and developers alike. Developers should find that Icy’s ‘EzPlug’ API library, versioning, and auditing tools make creating a custom plugin from most any source easy. Users will find the automatic error reporting, central repository and on-line community hub great for storing and sharing plugins and protocols. Icy is even developing a cloud-computing framework to address the scalability issues of high-content screening. As of this writing there are 207 plug-ins 50 scripts and 14 protocols available for download, including those for microscope control, particle tracking, three dimensional segmentation, and even spot detection using wavelets.

Published in Nature Methods (Nat Methods 9(7):690-6 (2012)). Icy can be downloaded at http://icy.bioimageanalysis.org/ Strength: Open-source. Centralized repository of 205 plugins, 50 scripts and 14 protocols

Rate and comment plugins 5D Search and install features directly from Icy Graphical programming with protocols Write scripts in javascript or python Automatic bug reports Native ImageJ integration 100% compatible Native Micro-Manager integration Share your plugins and protocols online Can run headless Intuitive user interface Online management of plugins Connect Icy to Matlab Interactive widgets Build your graphical interface with EzPlug Use the power of your graphic card with OpenCL Loaded with 20 up-to date libs Weaknesses No tutorial for plugins writing..yet See here: http://icy.bioimageanalysis.org/index.php?display=devDoc http://icy.bioimageanalysis.org/index.php?display=detailTag&tagId=29 and here: http://icy.bioimageanalysis.org/index.php?display=startDevWithIcy and also here: http://icy.bioimageanalysis.org/index.php?display=startDevWithIcy Image size limited to 2GigaByte per single 2D channel (means that an image of 40.000x40.000 can be handle by Icy. Still big !) Still you can have a stack of 100000x40Kx40kxUnlimited number of channel if you have RAM. Will be improved

Fiji is just ImageJ: a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. The main focus of Fiji is to assist research in life sciences. It is a free, open-source, community-driven project.

PALMsiever is a MATLAB-based application that allows the filtering (sieving) and analysis of localization-microscopy data. It provides the ability to render the data using different visualization algorithms and perform simple measurements on the point-localization data. It is extensible using simple MATLAB scripts and a number of plugins is already provided with the software itself, including a clustering algorithm and 3D rendering.

Strengths: intuitive, easy navigation through the point-localization data

Limitations: no multi-color