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Download Data

Here you may download the complete dataset contained in the YRC Public Image Repository.

Image Repository Data

strain_genotypes.txt
This tab delimited file contains a mapping of strain names to genotypes. It contains the following columns:
  • strain id - unique numerical identifier for a particular strain
  • strain name - unique string identifier for a particular strain (used in YRC PIR web site)
  • genotype - the genotype for a particular strain
proteins.fasta
A FASTA-formatted file containing protein names (used in YRC PIR), NCBI taxonomy IDs, descriptions and sequences.
Complete Data Download:
The entire YRC PIR has been archived into ten tarred and gzipped files for download. Each .tgz file may be uncompressed on Windows using WinZip, Apple OS X using Stuffit Expander and on Linux using the command line syntax "tar -xzf full_download_0.tgz".

The files will uncompress in the following format (this example assumes an experiment ID that ends in "123" and an experiment that includes 3 channels and 3 z-sections):

experiments/1/2/3/YRCPIR_ex123/
metadata.txt
images/
YRCPIR_123_p0_z0_c0_t0.ome.tiff
YRCPIR_123_p0_z0_c0_t0.txt
YRCPIR_123_p0_z0_c1_t0.ome.tiff
YRCPIR_123_p0_z0_c1_t0.txt
YRCPIR_123_p0_z0_c2_t0.ome.tiff
YRCPIR_123_p0_z0_c2_t0.txt
YRCPIR_123_p0_z1_c0_t0.ome.tiff
YRCPIR_123_p0_z1_c0_t0.txt
YRCPIR_123_p0_z1_c1_t0.ome.tiff
YRCPIR_123_p0_z1_c1_t0.txt
YRCPIR_123_p0_z1_c2_t0.ome.tiff
YRCPIR_123_p0_z1_c2_t0.txt
YRCPIR_123_p0_z2_c0_t0.ome.tiff
YRCPIR_123_p0_z2_c0_t0.txt
YRCPIR_123_p0_z2_c1_t0.ome.tiff
YRCPIR_123_p0_z2_c1_t0.txt
YRCPIR_123_p0_z2_c2_t0.ome.tiff
YRCPIR_123_p0_z2_c2_t0.txt

File definitions:
  • metadata.txt - contains metadata for the experiment. The data are clearly labeled in the text file.
  • images/YRCPIR_1_p0_z0_c0_t0.ome.tiff - an OME TIFF containing the image data. The OME-XML contained in the TIFF header contains image metadata. The filename is formatted to as: YRCPIR_EXPERIMENT ID_pPANEL INDEX_zZ-SECTION INDEX_cCHANNEL INDEX_tTIME INDEX.ome.tiff.
  • images/YRCPIR_1_p0_z0_c0_t0.txt - contains metadata for the given image. The data are clearly labeled in the text file.
Files:
NIH NIGMS NCRR
The YRC Public Image Repository is supported by grant P41 RR11823 from the National Center for Research Resources and grants P41GM103533 and GM40506 from National Institute of General Medical Sciences at the US National Institutes of Health.