The table presents a detailed comparison of the cellular image analysis tools available to the research community. While making the table a special attention was paid towards three key points:
1. Open source with community support, offering scripts and tools, for researchers with or without a programming knowledge;
2. Specific to DNA/RNA FISH analysis;
3. Ability to work in any environment: Linux, Mac OS or Windows;
4. Availability of modules for quantitative analysis.
If you use any data provided in this page, please cite the MuG project:
“MuG project H2020-676556 Oct. 2016 – from www.multiscalegenomics.eu”
This work uses data, tools or expertise provided by MuG (www.multiscalegenomics.eu) a project funded by the EU H2020 research and innovation programme: H2020-EINFRA-2015-1-676556
|
Tool |
Function |
Programming Language |
GUI |
OS (#) |
Availability |
Doc |
Source code |
Bio- |
Interactive / Flexibility |
Macros / Plugins Available |
Quantitative and Qualitative Analysis |
Ref |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Standalone platform to visualize, annotate and quantify bioimaging data |
Java |
Yes |
All |
Open source |
Yes |
Yes |
Yes |
Yes |
Yes |
Yes |
1 |
|
|
Standalone platform for quantitative analysis of biological images |
Java, C++ and Python |
Yes |
All |
Open source |
Yes |
Yes |
Yes |
Yes |
Yes |
Yes |
2 |
|
|
Analysis and visualization program for microbiology and microbial ecology |
C++ |
Yes |
Linux, Windows |
Open to Academia |
Yes |
NA |
NA |
NA |
NA |
Yes |
3 |
|
|
Software of the analysis of microbial ecology |
NA |
Yes |
Windows |
Free License |
Yes |
NA |
NA |
NA |
NA |
NA |
4 |
|
|
Open source image processing platform |
Java |
Yes |
All |
Open source |
Yes |
Yes |
Yes |
Yes |
Yes |
Yes |
5 |
|
|
3D imaging software |
NA |
Yes |
Mac OS, Windows |
Commercial License |
Yes |
No |
No |
Yes |
NA |
Yes |
||
|
Standalone tool for image Analysis |
NA |
Yes |
Windows |
Free License |
Yes |
No |
No |
No |
NA |
No |
||
|
Standalone tool for visualization and analysis of 3D and 4D microscopy datasets |
NA |
Yes |
Mac OS, Windows |
Commercial License |
Yes |
No |
Yes |
Yes |
NA |
Yes |
||
|
Cloud based software to view, organize, analyze and share image data. |
NA |
Yes |
All |
Open source |
Yes |
Yes |
Yes |
NA |
NA |
Yes |
6 |
|
|
Software to store, visualize, organize and analyze images in the cloud |
MATLAB, Python, Java+ImageJ |
Yes |
All |
Open Source |
Yes |
Yes |
Yes |
Yes |
NA |
Yes |
7 |
|
|
Tool to analyze single molecule mRNA FISH data |
MATLAB |
Yes |
All |
Open source |
Yes |
Yes |
NA |
NA |
NA |
Yes |
8 |
|
|
For automated analysis of FISH images |
MATLAB |
Yes |
All |
Open source |
Yes |
Yes |
NA |
NA |
NA |
Yes |
9 |
|
|
Tool to high-throughput processing and analysis of 3D fluorescence images |
Java, R (on FIJI) |
Yes |
All |
Open source |
Yes |
Yes |
NA |
NA |
NA |
Yes |
10 |
|
|
Automatic or semiautomatic FISh and CT analysis |
Java |
Yes |
All |
Open source |
Yes |
NA |
NA |
NA |
NA |
Yes |
11 |
|
|
Smart 3D-FISH |
An imageJ plugin to spot segmentation and distance measurements in FISH |
Java (FIJI) |
Yes |
All |
Open source |
Yes |
NA |
NA |
NA |
NA |
Yes |
12 |
|
IMACULAT |
Software package for quantitative analysis of chromosome localization in nucleus |
Perl (Plug-in) |
NA |
Linux |
Open source |
Yes |
NA |
NA |
NA |
NA |
Yes |
13 |
Table adapted from: Wiesmann et al., (2015) Review of free software tools for image analysis of fluorescence cell micrographs. Journal of Microscopy, 257(1), 39–53. http://onlinelibrary.wiley.com/doi/10.1111/jmi.12184/full.
Completed with https://omictools.com, and recent publications.
NA = Information not available
(#) “All” indicates available for Linux, Mac OS and Windows.
(*) Created by the Quantitative Image Analysis Unit at Institut Pasteur
(†) CellProfiler project team is based in the Carpenter Lab at the Broad Institute of Harvard and MIT.
(‡) CMEIAS is Copyrighted 1999-2016 Michigan State University Board of Trustees
(§) Commercial
(¶) University of Dundee & Open Microscopy Environment
(**) Center for Bio-Image Informatics, University of California, Santa Barbara
References
[1] de Chaumont et al., (2012) Icy: an open bioimage informatics platform for extended reproducible research. Nature Methods, 9(7) 690-6
[2] Lamprecht et al., (2007) CellProfiler: free, versatile software for automated biological image analysis. Biotechniques, 42(1), 71-75
[3] Daims H, Lücker S, Wagner M. (2006) daime, a novel image analysis program for microbial ecology and biofilm research. Environ. Microbiol., 8, 200-213
[4] Liu et al., (2001) CMEIAS: A computer-aided system for the image analysis of bacterial morphotypes in microbial communities. Microbial Ecology, 41(3), 173-194 (erratum in Microbial Ecology, 42(2), 215)
[5] Schneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012) NIH Image to ImageJ: 25 years of image analysis. Nature methods, 9(7), 671-675
[6] Johnston et al., (2006) A Flexible Framework for Web Interfaces to Image Databases: Supporting User-Defined Ontologies and Links to External Databases. 2006 IEEE International Symposium on Biomedical Imaging.
[7] Kvilekval et al., (2010) BisQue: A Platform for Bioimage Analysis and Management. Bioinformatics, &26(4), 544–552
[8] Mueller et al., (2016) FISH-quant: automatic counting of transcripts in 3D FISH images. Nature Methods, 10(4), 277-8
[9] Shirley et al., (2011) FISH Finder: a high-throughput tool for analyzing FISH images. Bioinformatics, 27(7), 933-8
[10] Ollion et al., (2013) TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization. Bioinformatics, 29(14), 1840-1
[11] Iannuccelli E., (2010) NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments. Bioinformatics, 26(5), 696-7
[12] Gue et al., (2005) Smart 3D-FISH: automation of distance analysis in nuclei of interphase cells by image processing. Cytometry Part A., 67(1), 18-26
[13] Mehta et al., (2013) IMACULAT – an open access package for the quantitative analysis of chromosome localization in the nucleus. PloS one, 8(4), e61386