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 - PLoS ONE 2012 - Classification and Reannotation

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

Jieyue Li, Justin Y. Newberg, Mathias Uhlen, Emma Lundberg, and Robert F. Murphy. Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas. (2012) PLoS ONE 7:e0050514.

The data and code are contained in the following files compressed with tar with the -z option (gzip)

Source Code
   HPA_reannotation_onlycode.tgz (3Mb)
Raw Data
   The .tgz files below contain the raw images for all proteins used in this study (they are each approximately 1 Gb). You can download individual files (an Excel file containing a list of which proteins are in each file can be found here), or you can use the helper script ( that downloads, concatenates and extracts all of the raw data.
Intermediate Results
   Results of classification and reannotation (used to regenerate tables and figures in the paper)
   HPA_reannotation_intermediate.tgz (1.6Gb)

Recreating Final 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 to the desired directory.
tar -xzf HPA_reannotation_onlycode.tgz

Download and expand one or more of the tgz files of raw images, e.g.:
tar -xzf HPA_reannotation_rawdataHPA_A431-1.tgz
You can also use the helper script to download and extract all of the raw images (approximately 70GB).

In Matlab, run the main script
>> masterscript
See details in masterscript.m for more options of input image path.

Recreating Final Results from Intermediate Results

Recreate the results from the article (i.e. the figures and tables), from intermediate results of classification and reannotation

To recreate the final results from the intermediate results of classification and reannotation, download the source code and intermediate results to the desired directory and expand them.
tar -xzf HPA_reannotation_onlycode.tgz
tar -xzf HPA_reannotation_intermediate.tgz

In Matlab, run the function
>> regenResults

System requirements

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

Last Updated: 02 Dec 2012

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