ProStack -
a platform for image processing and analysis
This work is
supported by NIH Grant
RR07801 and RFBR grants 09-04-001590-a,
08-04-00712-a
Description
ProStack provides flexible and convenient platform for processing of experimental images. It implements various image processing methods as separate modules. Several modules can be joined in a complex image processing scenario by use of a graphical user interface and the intermediate results can be visualized during the workflow enactment. The designed workflow can be saved as a complex program module and re-used in other workflows.
Due to an open architecture ProStack can be easily integrated with any package for image processing. Currently we have integrated ProStack with the Ontology of image processing methods, what simplifies the selection of an appropriate method, as well as with the Matlab Image Processing Toolbox.
ProStack is scalable and supports distributed processing and analysis of data.
- K. Kozlov (2008). ProStack, the image analysis software to process and quantify patterns of gene expression, Proceedings of Helmholtz Russian-German Workshop on Systems Biology, February 27-29, 2008, Moscow, p.44.
- K. Kozlov (2008). ProStack: a new platform for image analysis, CSHL Conference "Computational Cell Biology", March 24 - 31, 2008.
Read documentation on-line
Download ProStack:
GNU/Linux binaries 64 bit,
GNU/Linux binaries 64 bit with OpenMP acceleration,
Mac OS X 10.5 Leopard binaries,
MS Windows binaries 32 bit,
Sources,
User guide
Download workflow developed to segment the confocal images of segmentation gene expression patterns and movie, which demonstrates how to use it.
Download other workflows. You will need to correct paths by double-clicking on the nodes labeled INPUT.
Download workflows for processing of 3D images(stacks), the size is 206791064 bytes . You will need to correct paths by double-clicking on the nodes labeled INPUT and OUTPUT. The file descr.doc in the archive is description of workflows (currently only in Russian).
Check here for latest RPMS and sources.
Starting from version 2.3.0 the package contains methods for image deconvolution including blind deconvolution.
Download ProStack and unpack the archive to /usr/local if you are a superuser or to your home directory. Download sample workflows and run the script with the command from the terminal:
[user@machine ~]$ bash Downloads/isms_samples-1.9.51.sh
Running on GNU/Linux Run
ProStack with the command from the terminal: [user@machine ~]$ /path/to/directory/ProStack/bin/ProStack
Download ProStack dmg image and install it like any other Mac OS X software, i.e mount the dmg image and drag the ProStack.app to Application folder or any other folder.
Uninstall the previous version of ProStack if you have one and remove the directory ".bambu" from your home directory, e.g remove "C:\Documents and Settings\Administrator\.bambu". Download ProStack and run the script, install the package in the root directory of the drive, e.g. C:\ProStack.
Sample workflows are included in the distribution.
Running on Microsoft Windows Run
ProStack form the Start menu.
Installation on GNU/Linux
Installation on Mac OS X 10.5 Leopard
Installation on Microsoft Windows
The tool is implemented with
gnuplot,
gtk2+, Fedora Linux
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