The purpose of this work is to create a WIPP plugin for the segmentation of 3D microscopy images. See license for disclaimer.
src: contains the source Java codeDockerfileplugin.jsonWIPP plugin manifest
The project Java 8+ and Maven.
mvn clean package
docker build . -t wipp/wipp-3d-segmentation-plugin:0.0.1
From this directory:
python ./src/stardist-inference.py \
--inputImages ./sample-data/images \
--output ./sample-data/outputs
--pretrainedModel 2D_versatile_fluo
From this directory, assuming the images to process are in a folder "sample-data/images":
docker run -v "$PWD"/sample-data:/data \
wipp/wipp-3d-segmentation-plugin:0.0.1 \
--inputImages /data/images \
--output /data/outputs \
--threshold Otsu \
--removeEdgeComponents false \
--fillHoles false \
--makeSingleComponent false
-v: mounts a volume/folder from your machine inside of the Docker container
- register the plugin.json in a deployed WIPP instance - see https://github.com/usnistgov/WIPP
- upload input images as WIPP image collection
- create a workflow by adding one step called 3d-seg
- run and monitor the workflow execution
- download resulting WIPP image colection
- WIPP team, ITL NIST, Software and System Division, Information Systems Group
- Contact email address at NIST: wipp-team@nist.gov
Simon Jr., C. , Bajcsy, P. , Chalfoun, J. , Majurski, M. , Brady, M. , Simon, M. , Hotaling, N. , Schaub, N. , Horenberg, A. , Szczypinski, P. , Wang, D. , DeFelice, V. , Yoon, S. and Florczyk, S. (2023), Measuring Dimensionality of Cell-Scaffold Contacts of Primary Human Bone Marrow Stromal Cells Cultured on Electrospun Fiber Scaffolds, Journal of Biomedical Materials Research, [online], https://doi.org/10.1002/jbm.a.37449, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=934599 (Accessed February 10, 2023)