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Murphy Lab - Software - PLoS ONE 2012 - Microtubule Distribution Comparison

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

Jieyue Li, Aabid Shariff, Mikaela Wiking, Emma Lundberg, Gustavo K. Rohde and Robert F. Murphy. Estimating microtubule distributions from 2D immunofluorescence microscopy images reveals differences among human cultured cell lines. (2012) PLoS ONE 7:e0050292.

The data and code are contained in the following files compressed with tar and gzip

Source Code
   CellLines_Code.tgz (48Mb)
Raw Data
   Helper script (getrawdata.sh) that downloads, concatenates and extracts the raw data in the list below.
   CellLines_rawdataHPA_A431.tar.gz (246Mb)
   CellLines_rawdataHPA_A549.tar.gz (46Mb)
   CellLines_rawdataHPA_CaCo.tar.gz (79Mb)
   CellLines_rawdataHPA_Hek293.tar.gz (60Mb)
   CellLines_rawdataHPA_HeLa.tar.gz (346Mb)
   CellLines_rawdataHPA_HepG2.tar.gz (35Mb)
   CellLines_rawdataHPA_MCF7.tar.gz (45Mb)
   CellLines_rawdataHPA_PC3.tar.gz (177Mb)
   CellLines_rawdataHPA_RT4.tar.gz (46Mb)
   CellLines_rawdataHPA_U251MG.tar.gz (129Mb)
   CellLines_rawdataHPA_U2OS.tar.gz (203Mb)
Intermediate Results
   Results of estimated model parameters for microtubule distribution (used to regenerate tables and figures in the paper)
   CellLines_Results.tgz (130Mb)
   Masks for segmented single cells and shapes for cell geometries (cell shapes and nuclear shapes)
   CellLines_MasksShapes.tar.gz (1.1Gb)
Synthetic Images
   Helper script (getsyntheticimages.sh) that downloads, concatenates and extracts the generated images in the list below.
   Generated images of microtubule distribution for A-431 cell line from 2D HPA images.
   CellLines_ImagesHPA_A431.tar.gz.part-aa (1.9Gb)
   CellLines_ImagesHPA_A431.tar.gz.part-ab (1.9Gb)
   CellLines_ImagesHPA_A431.tar.gz.part-ac (1.9Gb)
   CellLines_ImagesHPA_A431.tar.gz.part-ad (1.9Gb)
   CellLines_ImagesHPA_A431.tar.gz.part-ae (1.9Gb)
   CellLines_ImagesHPA_A431.tar.gz.part-af (1.9Gb)
   CellLines_ImagesHPA_A431.tar.gz.part-ag (1.9Gb)
   CellLines_ImagesHPA_A431.tar.gz.part-ah (1.9Gb)
   CellLines_ImagesHPA_A431.tar.gz.part-ai (1.9Gb)
   CellLines_ImagesHPA_A431.tar.gz.part-aj (1.9Gb)
   CellLines_ImagesHPA_A431.tar.gz.part-ak (1.9Gb)
   CellLines_ImagesHPA_A431.tar.gz.part-al (1.9Gb)
   CellLines_ImagesHPA_A431.tar.gz.part-am (1.9Gb)
   CellLines_ImagesHPA_A431.tar.gz.part-an (37Mb)
   Generated images of microtubule distribution for U-2OS cell line from 2D HPA images.
   CellLines_ImagesHPA_U2OS.tar.gz.part-aa (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-ab (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-ac (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-ad (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-ae (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-af (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-ag (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-ah (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-ai (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-aj (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-ak (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-al (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-am (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-an (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-ao (1.9Gb)
   CellLines_ImagesHPA_U2OS.tar.gz.part-ap (720Mb)
   Generated images of microtubule distribution for U-251MG cell line from 2D HPA images.
   CellLines_ImagesHPA_U251MG.tar.gz.part-aa (1.9Gb)
   CellLines_ImagesHPA_U251MG.tar.gz.part-ab (1.9Gb)
   CellLines_ImagesHPA_U251MG.tar.gz.part-ac (1.9Gb)
   CellLines_ImagesHPA_U251MG.tar.gz.part-ad (1.9Gb)
   CellLines_ImagesHPA_U251MG.tar.gz.part-ae (1.9Gb)
   CellLines_ImagesHPA_U251MG.tar.gz.part-af (1.9Gb)
   CellLines_ImagesHPA_U251MG.tar.gz.part-ag (1.9Gb)
   CellLines_ImagesHPA_U251MG.tar.gz.part-ah (1.9Gb)
   CellLines_ImagesHPA_U251MG.tar.gz.part-ai (1.5Gb)
   Generated images of microtubule distribution for RT-4 cell line from 2D HPA images.
   CellLines_ImagesHPA_RT4.tar.gz.part-aa (1.9Gb)
   CellLines_ImagesHPA_RT4.tar.gz.part-ab (1.9Gb)
   CellLines_ImagesHPA_RT4.tar.gz.part-ac (1.9Gb)
   CellLines_ImagesHPA_RT4.tar.gz.part-ad (1.9Gb)
   CellLines_ImagesHPA_RT4.tar.gz.part-ae (423Mb)
   Generated images of microtubule distribution for PC-3 cell line from 2D HPA images.
   CellLines_ImagesHPA_PC3.tar.gz.part-aa (1.9Gb)
   CellLines_ImagesHPA_PC3.tar.gz.part-ab (1.9Gb)
   CellLines_ImagesHPA_PC3.tar.gz.part-ac (1.9Gb)
   CellLines_ImagesHPA_PC3.tar.gz.part-ad (1.9Gb)
   CellLines_ImagesHPA_PC3.tar.gz.part-ae (1.9Gb)
   CellLines_ImagesHPA_PC3.tar.gz.part-af (1.9Gb)
   CellLines_ImagesHPA_PC3.tar.gz.part-ag (1.9Gb)
   CellLines_ImagesHPA_PC3.tar.gz.part-ah (1.9Gb)
   CellLines_ImagesHPA_PC3.tar.gz.part-ai (1.9Gb)
   CellLines_ImagesHPA_PC3.tar.gz.part-aj (1.9Gb)
   CellLines_ImagesHPA_PC3.tar.gz.part-ak (1.9Gb)
   CellLines_ImagesHPA_PC3.tar.gz.part-al (1.9Gb)
   CellLines_ImagesHPA_PC3.tar.gz.part-am (1.9Gb)
   CellLines_ImagesHPA_PC3.tar.gz.part-an (43Mb)
   Generated images of microtubule distribution for Hep-G2 cell line from 2D HPA images.
   CellLines_ImagesHPA_HepG2.tar.gz.part-aa (1.9Gb)
   CellLines_ImagesHPA_HepG2.tar.gz.part-ab (1.9Gb)
   CellLines_ImagesHPA_HepG2.tar.gz.part-ac (1.9Gb)
   CellLines_ImagesHPA_HepG2.tar.gz.part-ad (1.2Gb)
   Generated images of microtubule distribution for HeLa cell line from 2D HPA images.
   CellLines_ImagesHPA_HeLa.tar.gz.part-aa (1.9Gb)
   CellLines_ImagesHPA_HeLa.tar.gz.part-ab (1.9Gb)
   CellLines_ImagesHPA_HeLa.tar.gz.part-ac (1.9Gb)
   CellLines_ImagesHPA_HeLa.tar.gz.part-ad (1.9Gb)
   CellLines_ImagesHPA_HeLa.tar.gz.part-ae (1.9Gb)
   CellLines_ImagesHPA_HeLa.tar.gz.part-af (1.9Gb)
   CellLines_ImagesHPA_HeLa.tar.gz.part-ag (1.9Gb)
   CellLines_ImagesHPA_HeLa.tar.gz.part-ah (1.9Gb)
   CellLines_ImagesHPA_HeLa.tar.gz.part-ai (1.9Gb)
   CellLines_ImagesHPA_HeLa.tar.gz.part-aj (1.9Gb)
   CellLines_ImagesHPA_HeLa.tar.gz.part-ak (348Mb)
   Generated images of microtubule distribution for CaCo2 cell line from 2D HPA images.
   CellLines_ImagesHPA_CaCo2.tar.gz.part-aa (1.9Gb)
   CellLines_ImagesHPA_CaCo2.tar.gz.part-ab (1.9Gb)
   CellLines_ImagesHPA_CaCo2.tar.gz.part-ac (1.9Gb)
   CellLines_ImagesHPA_CaCo2.tar.gz.part-ad (1.9Gb)
   CellLines_ImagesHPA_CaCo2.tar.gz.part-ae (1.9Gb)
   CellLines_ImagesHPA_CaCo2.tar.gz.part-af (1.9Gb)
   CellLines_ImagesHPA_CaCo2.tar.gz.part-ag (1.9Gb)
   CellLines_ImagesHPA_CaCo2.tar.gz.part-ah (371Mb)
   Generated images of microtubule distribution for A-549 cell line from 2D HPA images.
   CellLines_ImagesHPA_A549.tar.gz.part-aa (1.9Gb)
   CellLines_ImagesHPA_A549.tar.gz.part-ab (1.9Gb)
   CellLines_ImagesHPA_A549.tar.gz.part-ac (1.9Gb)
   CellLines_ImagesHPA_A549.tar.gz.part-ad (1.9Gb)
   CellLines_ImagesHPA_A549.tar.gz.part-ae (1.9Gb)
   CellLines_ImagesHPA_A549.tar.gz.part-af (899Mb)
   Generated images of microtubule distribution for Hek-293 cell line from 2D HPA images.
   CellLines_ImagesHPA_Hek293.tar.gz.part-aa (1.9Gb)
   CellLines_ImagesHPA_Hek293.tar.gz.part-ab (1.9Gb)
   CellLines_ImagesHPA_Hek293.tar.gz.part-ac (1.9Gb)
   CellLines_ImagesHPA_Hek293.tar.gz.part-ad (1.9Gb)
   CellLines_ImagesHPA_Hek293.tar.gz.part-ae (1.9Gb)
   CellLines_ImagesHPA_Hek293.tar.gz.part-af (1000Mb)
   Generated images of microtubule distribution for MCF-7 cell line from 2D HPA images.
   CellLines_ImagesHPA_MCF7.tar.gz.part-aa (1.9Gb)
   CellLines_ImagesHPA_MCF7.tar.gz.part-ab (1.9Gb)
   CellLines_ImagesHPA_MCF7.tar.gz.part-ac (1.9Gb)
   CellLines_ImagesHPA_MCF7.tar.gz.part-ad (1.9Gb)
   CellLines_ImagesHPA_MCF7.tar.gz.part-ae (1.8Gb)
   Generated images of microtubule distribution for 2D central slices of HeLa 3D images.
   CellLines_ImagesHeLa2D.tar.gz.part-aa (1.9Gb)
   CellLines_ImagesHeLa2D.tar.gz.part-ab (1.9Gb)
   CellLines_ImagesHeLa2D.tar.gz.part-ac (1.9Gb)
   CellLines_ImagesHeLa2D.tar.gz.part-ad (1.9Gb)
   CellLines_ImagesHeLa2D.tar.gz.part-ae (788Mb)
   Generated images of microtubule distribution for HeLa 3D images.
   CellLines_ImagesHeLa3D.tar.gz (1.5Gb)

Recreating Results from Raw Image Data

To recreate the results from the article (i.e. the figures and tables) from the raw image data,

Download and expand the source code file above to the desired directory.
tar -xzf CellLines_Code.tar.gz

Download and expand the raw images for one or more of the cell lines, e.g.
tar -xzf CellLines_rawdataHPA_A431.tar.gz
This extracts the files into the appropriate subdirectory in the images subdirectory of the CellLines directory. You can also use the helper script getrawdata.sh to download and extract these files.

In Matlab, run the main function
>> masterscript
See details in masterscript.m for more options of input image path and selection of cell line(s).

Recreating Results from Intermediate Results

Option 1: Recreate the results from the article (i.e. the figures and tables), from intermediate results of segmented cell geometries (masks, cell and nuclear shapes)

To recreate the results from the article, from intermediate results of segmented cell geometries (masks, cell and nuclear shapes)
Download and extract the source code and intermediate results from the above links to the desired directory
tar -xzf CellLines_Code.tar.gz
tar -xzf CellLines_MasksShapes.tar.gz

In Matlab, run the main function - masterscript, e.g.
>> masterscript

See details in masterscript.m for more options of input image path and selection of cell line(s).

Option 2: Recreate the results from the article (i.e. the figures and tables), from intermediate results of generated images and calculated features

To recreate the results from the article, from intermediate results of generated images and calculated features download the source code and intermediate results of generated images and calculated features (you may choose one or more cell lines) from the above links to the desired directory.
tar -xzf CellLines_Code.tar.gz
Concatenate and expand the generated images
cat CellLines_ImagesHPA_A431.tar.gz.part-* > CellLines_ImagesHPA_A431.tar.gz
tar -xzf CellLines_ImagesHPA_A431.tar.gz
You can use the helpder script getsyntheticimages.sh to download, concatenate and extract these files.

In Matlab, run the main function
>> masterscript

See details in masterscript.m for more options of input image path and selection of cell line(s).

Option 3: Recreate the results from the article, i.e. the figures and tables, from intermediate results of all estimated model parameters

To recreate the results from the article from intermediate results of all estimated model parameters download the source code and estimated model parameters from the above link to the desired directory
tar -xzf CellLines_Code.tar.gz

Expand the intermediate results of all estimated model parameters
tar -xzf CellLines_Results.tgz

In Matlab, run the function
>> regenResults

System requirements

  • MATLAB
This package has been tested using Matlab 2011a under CentOS in a 64bit architecture.


Last Updated: 28 Nov 2012




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