TABLE I.
Open source codes used in quantitative analyses of striated tissue.
| Name | Language | Capabilities | Key measures | Link to code |
|---|---|---|---|---|
| ConTraX38 | Matlab | Dynamic | Over time tracking of contractile dynamics of thousands of cells and quantifying cell area | https://github.com/MicrosystemsLab/ContraX |
| SarcTrack61 | Matlab | Dynamic | Quantifying sarcomere length and content, as well as contraction and relaxation parameters | https://github.com/HMS-IDAC/SarcTrack |
| SOTA29 | Matlab | Static | Cell segmentation and sarcomere registration | http://bme.virginia.edu/saucerman/ a |
| Z-line detection60 | Matlab | Static, ∼dynamic | Segmention and analysis of sarcomeric z-discs | https://github.com/Cardiovascular-Modeling-Laboratory/zlineDetection |
| Deepsynth64 | ImageJ | Static | Nuclei segmentation | https://github.com/grockious/deepsynth |
| LoS65 | Mathematica | Dynamic | 3D fluorescent nuclei segmentation | www.physikalischebiologie.de/downloads |
| OpenSegSPIM66 | Matlab | Static | Nuclei segmentation of confocal, multiphoton, and LSFM data | opensegspim.weebly.com |
| Other resources the reader might be interested in | ||||
| SarCoptiM62 | ImageJ | Dynamic | Computation of spatial frequency of the striated pattern of a myocyte | https://pccv.univ-tours.fr/ImageJ/SarcOptiM/dl/SarcOptiM.zip |
| Sarc-Graph59 | Python | Dynamic | Segmentation, tracking and analysis of sarcomeres | https://github.com/elejeune11/Sarc-Graph |
| TANGO67 | ImageJ and R | Static | Quantitative study of nuclear organization in fluorescent images | http://biophysique.mnhn.fr/tango |
| MINS68 | Matlab/C++ | Static | 2D and 3D segmentation of cells and nuclei detection | http://katlab-tools.org |
| RACE69 | C++ | Static | 3D cell segmentation for confocal and LSFM data | https://bitbucket.org/jstegmaier/race/downloads/ |
| SAMA70 | ImageJ/R | Dynamic | Quantitative and morphological 3D analysis of cell structure | https://montevil.theobio.org/en/content/sama a |
| Vaa3D71 | Qt/C++ | Dynamic | 3D visualization of gigabyte-sized microscopy images | https://github.com/Vaa3D/Vaa3D_Wiki/wiki/Download-Vaa3D-executables |
| 3D-cell-annotator72 | MITK | Static | 3D segmentation and annotation of single cells | www.3d-cell-annotator.org |
| XPIWIT73 | Qt/C++ | Static | 3D+t segmentation of fluorescent nuclei | https://bitbucket.org/jstegmaier/xpiwit/downloads/ |
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