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WIPP-3d-segmentation-plugin

Statements of purpose and maturity

The purpose of this work is to create a WIPP plugin for the segmentation of 3D microscopy images. See license for disclaimer.

Description of the repository contents

  • src: contains the source Java code
  • Dockerfile
  • plugin.json WIPP plugin manifest

Technical installation instructions, including operating system or software dependencies

The project Java 8+ and Maven.

Installation (optional if using the pre-built Docker image)

Build JAR

mvn clean package

Build the Docker image

docker build . -t wipp/wipp-3d-segmentation-plugin:0.0.1

Execution

Run the Python code

From this directory:

python ./src/stardist-inference.py \
--inputImages ./sample-data/images \
--output ./sample-data/outputs
--pretrainedModel 2D_versatile_fluo

Run the Docker image

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

Run the WIPP plugin

- 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

Additional Information

Contact information

  • WIPP team, ITL NIST, Software and System Division, Information Systems Group
  • Contact email address at NIST: wipp-team@nist.gov

Related Material

Citation:

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)

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A WIPP plugin for segmenting 3D images

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