cellBASE image conversion

This document explains how the image conversion in cellBASE is done. (For developers: the conversion is done in the file include/web/imageset_common.inc.php:491)

First, the script checks if the given folder is a known format. Then it calls the conversion script from /bin/converters (scanr2ometif, msa2ometif or one from converters dir) with a microscope-in file as parameter.

  • scanR: The script scanr2ometif checks if the file 'experiment_descriptor.xml' exists. And if so, it calls bfconvert from bio-formats to do the conversion.
    bfconvert $params "$1/experiment_descriptor.xml" "$outdir/${1:t}/NaVt––ZNaVc.ome.tif(with $params setting the compression or not)
  • MSA: The script mas2ometif checks if the file 'input/AdditionalData/LIF2OME.xml' exists. After that, the php script msaconvert is called with:
    msaconvert.php -infile path/to/microscope-in-file < inputadditionaldatalif2ome.xml >
    The script expects the images to be already in ome.tif format. It only changes the names of and file structure of the existing sp5 output.
  • Zeiss: The script 'bin/converters/defaultLSM.php' converts images coming from a Zeiss microscope to OME.tiff.
    It needs to be called with: defaultLSM.php
    The filenames is expected to be something like: 002––02––(1,2––)s7424––INCENP––01.lsm
    If your structure is different we need to create a conversion tool for you. For that, please contact sauer@embl.de