Cytometry Development Workshop
Carnegie Mellon University
Computational Biology Department
Center for Bioimage Informatics
Biological Sciences Department
Biomedical Engineering Department
Machine Learning Department
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Lab Research Topics
Software and Documentation
Michael Boland's thesis
Murphy Lab - Software - Science Signaling 2016 - T cell Models
The software and intermediate results used for the following paper can be downloaded below:
K. T. Roybal, T. E. Buck, X. Ruan, B. H. Cho, D. J. Clark, R. Ambler, H. M. Tunbridge, J. Zhang, P. Verkade, C. Wülfing, and R. F. Murphy (2016) Computational spatiotemporal analysis identifies WAVE2 and Cofilin as joint regulators of costimulation-mediated T cell actin dynamics. Science Signaling 9:rs3. DOI: 10.1126/scisignal.aad4149
This source code is released under
GNU LGPL v2.1.
This file contains all source code, including open source packages listed below.
Primary image and annotation data can be downloaded here. The source code contains a Matlab script to download all of these files (see instructions below).
These files can be used to regenerate the tables and figures in the paper.
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/2016_TcellModels/Tcell_source_code.tgz
tar -xzf Tcell_source_code.tgz
- Download and expand the annotation files to the same directory.
wget -nc http://murphylab.web.cmu.edu/data/TcellModels/Tcell_annotations.tgz
tar -xzf Tcell_annotations.tgz
- (optional) Download and expand the intermediate result files to the same directory. These files occupy 107 GB. Having these files avoids having to segment and align the individual cell frames. This process takes approximately 1300 hours on a single cpu.
wget -nc http://murphylab.web.cmu.edu/software/2016_TcellModels/Tcell_intermediate_results.tgz
tar -xzf Tcell_intermediate_results.tgz
- Download and expand the images to the same directory using the script provided in the source code (these files occupy 153 GB).
- Run the main script. Note that the script will skip any steps for a given sensor and condition for which files are already present in the intermediate results. If primary data are not available for a given sensor and condition, the masterscript will warn about the missing data but will process other sensors and conditions if present. Thus the results for just one sensor can be reproduced by downloading the primary data for just that sensor/condition (and optionally the entire intermediate results); this will produce only the files (e.g., maps) for that sensor/condition.
The total run time for the script is approximately 6100 hours on a single cpu beginning from the raw images (if intermediate results are not present) or 3 hours beginning from the intermediate results.
This package has been tested using Matlab 2015a in CentOS.
Open source packages used
- BasicSnake by Dirk-Jan Kroon
- bitmap_plot and isocontour by Dirk-Jan Kroon
- bonf_holm by David Groppe
- boundedline by Kelly Kearney
- cellstructeq and rotateXLabels by The MathWorks Ltd.
- coherencefilter by Dirk-Jan Kroon, Pascal Getreuer
- convnfft by Bruno Luong
- convolution3D_FFTdomain by Christopher Coello
- cvip_pgmtextur by Gregory Hance
- DataHash by Jan Simon
- dirr by Maximilien Chaumon
- discretesample by Dahua Lin
- distcorr by Shen Liu
- distinguishable_colors by Timothy E. Holy
- export_fig by Oliver J. Woodford, Yair M. Altman
- FATHOM Toolbox for Matlab by D. L. Jones
- fitcircle by Richard Brown
- freezeColors by John Iversen
- geom3d by INRA
- GrTheory by Sergii Iglin
- histwc by Mehmet Suzen
- img2vol by Joe Conti
- inhull by John D'Errico
- Inpaint_nans by John D'Errico
- inpolyhedron by Sven Holcombe
- libsvm-3.14 by Chih-Chung Chang and Chih-Jen Lin
- lowess by Jeff Burkey
- lowner by Anye Li
- Mesh_voxelisation by Adam H. Aitkenhead
- mirt3D_mexinterp by Andriy Myronenko
- mirt3D_mexinterp by Andriy Myronenko
- netlab by Ian T. Nabney
- NIFTI_20121012, affine, and bresenham_line3d by Jimmy Shen
- plotboxpos by Kelly Kearney
- pmkmp by Matteo Niccoli
- sort_nat by Douglas M. Schwarz
- tiffread by Francois Nedelec, EMBL
- toolbox_fast_marching, toolbox_graph, and toolbox_wavelet_meshes by Gabriel Peyre
- Uniform_Sampling_of_S2 by Anton Semechko
- vol3d by Joe Conti
- XYrotalabel by David Powers