Murphy Lab

 Cytometry Development Workshop

 Flow Cytometry



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

Murphy Lab - Software - Journal of Proteome Research 2008 HPA Analysis

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

J. Newberg and R. F. Murphy (2008). A Framework for the Automated Analysis of Subcellular Patterns in Human Protein Atlas Images. J. Proteome Res. 7:2300-2308.

The Matlab code can be downloaded here (236 KB). It contains a README file with instructions for downloading the primary data from the Human Protein Atlas, as well as a matlab script, downloadImages.m, that will automate the download. This also contains a script processData.m that will perform all necessary processing of image data (the images are not included with the code, see below), and makeFiguresAndTables.m, which will generate results from intermediate data (not included in this file, see below).

The original images, in addition to being downloadable from the Human Protein Atlas site, can be downloaded here (1.4 GB). The contents of this gzipped file must be placed in the 'data' directory of the accompanying code.

Intermediate results can be generated by running the processData.m function in the codebase (mentioned above). They can also simply be downloaded here (802 MB). To use these, place the contents of this unzipped file in the 'data' directory under the directory containing the Matlab code. The figures can then be generated using the makeFiguresAndTables.m script.

System requirements

The scripts were written for Matlab version 7.1 on Linux. The statistics, wavelet, and image processing toolboxes for Matlab are also required.

Tools created by others that are included in the code distribution for convenience


Last Updated: 08 Jun 2008

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