Segmentation-challenge

Getting started

A description of the overall challenge and the datasets can be found here.

Guidance on the expected format of the segmentation output can be found in the following file: Guidance on deliverables.docx

We have set up some sample code using the Allen Institute's Cell and Structure Segmenter framework.

The code is set up in Jupyter notebooks (readable in Jupyter Lab available within each instance during the hackathon).

To function properly you will need to correctly define DATAPATH

Within each notebook, define DATAPATH as the top directory containing the example (or full) image datasets. This currently works for an instance where the data were uploaded into the same directory as the notebook files. Please ensure you do NOT push any of the images to GitHub.

List of example code files

• test_Harvard_Lung.ipynb
• test_UNC_PCNA.ipynb
• test_Vanderbilt_colon.ipynb
• test_Vanderbilt_live_cell.ipynb