Thresholding plugin

Building

To build from source code, run ./mvn-packager.sh

The pre-built jar file can be found in the target folder.

To build the Docker image for the thresholding plugin, run docker build -t wipp-thresh-plugin or ./build-docker.sh.

Thresholdtype options

The options are documented at https://imagej.net/Auto_Threshold. We are currently supporting:

Manual,
IJDefault,
Huang,
Huang2,
Intermodes,
IsoData,
Li,
MaxEntropy,
Mean,
MinErrorI,
Minimum,
Moments,
Otsu,
Percentile,
RenyiEntropy,
Shanbhag,
Triangle,
Yen

Run the plugin

Manually

docker run -v /path/to/data:/data wipp-thresh-plugin \
  --input /data/input \
  --thresholdtype Manual \
  --thresholdvalue 150 \
  --output /data/output

Note: threshvalue is needed only if thresholdtype is set to Manual.

Using Argo

argo submit ./workflow-sample.yaml