Imaging utilities released by the Parker Institute for Cancer Immunotherapy.
Download from releases.
$ java -jar image-utils-0.1.0-standalone.jar [command] [args]
If you are working with large images, you may need to increase the maximum heap size.
java -Xmx16G -jar image-utils-0.1.0-standalone.jar [command] [args]
$ java -jar image-utils-0.1.0-standalone.jar split-hyperstack [args]
Splits a tiff hyperstack into individual tiffs. Accepts the following options:
-i or --input
Required. Either a tiff file or a directory containing multiple tiff files to be split.
-o or --outpath
Optional. A folder to write the output files to. Will create if it does not exist. Defaults to the parent folder of the tiff being split.
-s or --subfolder
Optional. If used, generates a folder for each tiff being split and puts the individual tiffs in the subfolder instead of alongside the parent tiff. Tiffs will be named only for the channel and not contain the sample name.
$ java -jar image-utils-0.1.0-standalone.jar split-tiled [args]
Splits a tiled tiff into individual tiffs.
-i or --input
Required. Either a tiff file or a directory containing multiple tiff files to be split.
-o or --outpath
Optional. A folder to write the output files to. Will create if it does not exist. Defaults to the parent folder of the tiff being split.
-s or --subfolder
Optional. If used, generates a folder for each tiff being split and puts the individual tiffs in the subfolder instead of alongside the parent tiff. Tiffs will be named only for the channel and not contain the sample name.
Outputs help and usage information.
Released under Apache 2 license. See the LICENSE file for details.