[an error occurred while processing this directive]

Murphy Lab

Home
Information
People
Addresses
Cytometry Development Workshop
FCS API

Research
Projects
Publications
Software
Presentations
Flow Cytometry

Affiliations
Carnegie Mellon University
Computational Biology Department
Center for Bioimage Informatics
Biological Sciences Department
Biomedical Engineering Department
Machine Learning Department
MBIC

[an error occurred while processing this directive]

Internal

Information
Lab FAQ
Lab Research Topics

Services
TypIX

Web Pages
Web Page Template
Visitation Statistics
Important Links

Software and Documentation
Matlab Docs
Khoros Docs
TN-Image Docs
Michael Boland's thesis

Murphy Lab - Software - MBoC 2015 - Cell and Nuclear Shape Models

The software and intermediate results used for the following paper can be downloaded below:

G. R. Johnson, T. E. Buck, D. P. Sullivan, G. K. Rohde, and R. F. Murphy (2015) Joint modeling of cell and nuclear shape variation. Molecular Biology of the Cell 26: 4046-4056. http://dx.doi.org/10.1091/mbc.E15-06-0370

License

This source code is released under GNU LGPL v2.1.

Downloads

Source Code

MBoC_Shape_source_code.tgz [100 MB]

Primary Data

Data for HeLa cells, from M. Velliste and R.F. Murphy (2002) Automated Determination of Protein Subcellular Locations from 3D Fluorescence Microscope Images. Proc 2002 IEEE Intl Symp Biomed Imaging (ISBI 2002), pp. 867-870. DOI:10.1109/ISBI.2002.1029397
- MBoC_Shape_hela_images.tgz [2.1 G]
Data for H1299 cells expressing different tagged proteins, from Frenkel-Morgenstern M, Cohen AA, Geva-Zatorsky N, Eden E, Prilusky J, Issaeva I, Sigal A, Cohen-Saidon C, Liron Y, Cohen L, Danon T, Perzov N, Alon U. (2009) Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells. Nucleic Acids Res. 38:D508-12. DOI:10.1093/nar/gkp808.
- MBoC_Shape_h1299_images.tgz [17 GB]
Data for MCF7 cells, from image set BBBC021v1 [Caie et al., Molecular Cancer Therapeutics, 2010], available from the Broad Bioimage Benchmark Collection [Ljosa et al., Nature Methods, 2012].
- MBoC_Shape_mcf7_images.tgz [123 MB]

Intermediate Results

These files can be used to regenerate the tables and figures in the paper.

MBoC_Shape_hela_intermediate_results.tgz [5.3 GB]
MBoC_Shape_h1299_intermediate_results.tgz [95 GB]
MBoC_Shape_mcf7_intermediate_results.tgz [3.3 GB]

Recreating results

To recreate the results from the article (i.e. the figures and tables),
Download and expand the source code to the desired directory.

wget -nc http://murphylab.web.cmu.edu/software/2015_MBoC_Cell_And_Nuclear_Shape/MBoC_Shape_source_code.tgz tar -xzf MBoC_Shape_source_code.tgz Either download and expand the primary data into the same root directory. wget -nc http://murphylab.web.cmu.edu/software/2015_MBoC_Cell_And_Nuclear_Shape/MBoC_Shape_hela_images.tgz wget -nc http://murphylab.web.cmu.edu/software/2015_MBoC_Cell_And_Nuclear_Shape/MBoC_Shape_h1299_images.tgz wget -nc http://murphylab.web.cmu.edu/software/2015_MBoC_Cell_And_Nuclear_Shape/MBoC_Shape_mcf7_images.tgz for FILE in *images*.tgz; do tar -xvf "$FILE"; done

Or download and expand the intermediate results into the same root directory.

wget -nc http://murphylab.web.cmu.edu/software/2015_MBoC_Cell_And_Nuclear_Shape/MBoC_Shape_h1299_intermediate_results.tgz wget -nc http://murphylab.web.cmu.edu/software/2015_MBoC_Cell_And_Nuclear_Shape/MBoC_Shape_hela_intermediate_results.tgz wget -nc http://murphylab.web.cmu.edu/software/2015_MBoC_Cell_And_Nuclear_Shape/MBoC_Shape_mcf7_intermediate_results.tgz for FILE in *results*.tgz; do tar -xvf "$FILE"; done

Go into the code directory and run the code

cd code matlab< >> masterscript

Note that the masterscript will check for the presence of the intermediate results files and if they are present it will skip processing of the corresponding primary data. If neither the primary data nor the intermediate results are present for a given cell line, the masterscript will warn about the missing data but will process data for other cell lines if present. Thus the results for just one cell line can be reproduced by downloading either primary data or intermediate results for that cell line.

System requirements

MATLAB

This package has been tested using Matlab 2014a in CentOS.

Last Updated: 07 Mar 2016