LIF is a grouped-stack file format containing multiple stacks. One could access each stack by LOCI Bio-Format plugin installed to ImageJ, but when file size is huge and data is in data server, data transfer rate becomes a bottle neck for the progress of 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. Following command will do the job, converting all.

sh /g/almf/software/bftools/bfconvert <filename.lif>   converted_%s_%n_C%c.tiff

One missing function with this CL tool 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, following shell script was created to transfer physical scales in together with conversion.

sh /g/almf/software/ij/lifcon.sh </full/path/to/file.lif>

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.

Bioformat commandline tool “showinf” is used to save metadata as a text file. Then During the extraction of tiff stacks, physical scales and dimensionality information is extracted from the text and applied to the tiff stack.

Since macro command run(“Properties…”, arg1, arg2) does not work when IJ is headless since Properties command uses AWT. To avoid this, a small plugin (that does not appear in the menu) was created for setting image properties. This plugin is called from macro to set physical scales.

Link for the Image Property setter.

#!/bin/sh
#script for converting Lif file to tif, and set physical scale.  
#
imgfullpath=$1

# path to IJ jar file
IJJARS="/g/almf/software/ij"

# path to image 
IMGFILE="${imgfullpath##*/}"
IMGPATH="${imgfullpath%/*}"
METAFULLPATH="${imgfullpath}.meta.txt"
echo ${METAFULLPATH}

# Lif converting IJ macro name
IJMACRONAME="LifOpenerCUI.ijm"

#timer
jobstart=$(date +%s)

sh /g/almf/software/bftools/showinf -nopix -nocore ${imgfullpath}>${METAFULLPATH}

chmod ugo+x ${METAFULLPATH}

/usr/struct/bin/java -cp ${IJJARS}/headless.jar:${IJJARS}/ij-1.44h.jar -Djava.awt.headless=true ij.ImageJ -ijpath ${IJ
JARS} -batch ${IJJARS}/${IJMACRONAME} ${imgfullpath}

# timer
jobend=$(date +%s)
echo "Time: $((jobend-jobstart)) secs."

To convert a file between formats, run: bfconvert [-debug] [-stitch] [-separate] [-merge] [-expand] [-bigtiff] [-compression codec] [-series series] [-map id] in_file out_file -debug: turn on debugging output -stitch: stitch input files with similar names -separate: split RGB images into separate channels -merge: combine separate channels into RGB image -expand: expand indexed color to RGB -bigtiff: force BigTIFF files to be written -compression: specify the codec to use when saving images -series: specify which image series to convert -map: specify file on disk to which name should be mapped If any of the following patterns are present in out_file, they will be replaced with the indicated metadata value from the input file. Pattern: Metadata value: ————————— %s series index %n series name %c channel index %w channel name %z Z index %t T index If any of these patterns are present, then the images to be saved will be split into multiple files. For example, if the input file contains 5 Z sections and 3 timepoints, and out_file is converted_Z%z_T%t.tiff then 15 files will be created, with the names converted_Z0_T0.tiff converted_Z0_T1.tiff converted_Z0_T2.tiff converted_Z1_T0.tiff … converted_Z4_T2.tiff Each file would have a single image plane.