LIF is a grouped-stack file format containing multiple stacks. One could access each of these stacks by LOCI Bio-Format plugin on desktop, but when file size is huge and data is in data server, data transfer rate becomes a bottle neck for the work.

TO avoid this, one could do the file conversion via command line. This could be done by “bfconvert” command line tool available from Bio-format web site, but its problem is that physical scales in x, y and z are not read out from LIF so that resulting Tiff stacks are devoid of these parameters. In addition, dimensional values such as number of slices per time point, and number of time points are not converted.

For this reason, use following shell script. <code> sh /g/almf/software/ij/lifcon.sh </full/path/to/file.lif> <code> This script will extract metadata from LIF, convert each stack to Tiff stack, and set the physical parameters of the image by extracting these values from metadata. Tiff stack will be saved under a newly created directly where the LIF is located. Name of the directory will be

<file.lif>_tifStack

A text file named

<filename.lif>.meta.txt is also generated, where extracted metadata is stored.