sauron is a software package which finds ring-like regions of increased density from one channel (Green) over another (Red) of a tiff file.
sauron can be installed with python3 setup.py install.
sauron can be used to search for rings on all Z-slices of a .tiff file in parallel.
$ sauron -h
Usage: sauron -d datadir -i imgname -r r_num -g g_num -t tmpdir -o outdir
[-M nMB] [-P project_name] [-J job_name] [-Z nZs] [-h]
datadir ........ Directory where input .tif files are located
imgname ........ Base name of .tif files (without R/G specified suffixes)
r_num .......... Name of red signal (ex. A640)
g_num .......... Name of green signal (ex. A488)
tmpdir ......... Location where temporary data should be stored
imgdir ......... Location where final cell images should be stored
nMB ............ Number of MB to be requested from LSF (default: 500)
project_name ... Project name to submit with (default: sauron)
jobname ........ Job name to submit with (default: sauron)
nZs ............ Number of Z stacks (default: 100)
saruman is called by sauro on each slice, but can also be used interactively to search for rings on a specific slice.
$ saruman -h
usage: Saruman [-h] -r RED_FILE -g GREEN_FILE -z IZ -t TMPDIR -o OUTDIR
optional arguments:
-h, --help show this help message and exit
-r RED_FILE, --red_file RED_FILE
TIF file containing red signal.
-g GREEN_FILE, --green_file GREEN_FILE
TIF file containing green signal.
-z IZ, --iz IZ Z stack to analyze.
-t TMPDIR, --tmpdir TMPDIR
Pre-existing tmp directory to use.
-o OUTDIR, --outdir OUTDIR
Pre-existing output directory to use.
Example data can be found in tests/data and tests can be run from the root directory
with python3 -m unittest discover tests test*.py from the root directory.