Digital Pathology Solution Accelerator

https://www.databricks.com/solutions/accelerators/digital-pathology

The tumor proliferation speed or tumor growth is an important biomarker for predicting patient outcomes. Proper assessment of this biomarker is crucial for informing the decisions for the treatment plan for the patient. In a clinical setting, the most common method is to count mitotic figures under a microscope by a pathologist. The manual counting and subjectivity of the process pose a reproducibility challenge. This has been the main motivation for many efforts to automate this process and use advanced ML techniques.

One of the main challenges however for automating this task, is the fact that whole slide images are rather large. WSI images can vary anywhere between 0.5 to 3.5GB in size, and that can slow down the image preprocessing step which is necessary for any downstream ML application.

In this solution accelerator, we walk you through a step-by-step process to use databricks capabilities to perform image segmentation and pre-processing on WSI and train a binary classifier that produces a metastasis probability map over a whole slide image (WSI).

Click on the "Get instant access" button in the top right corner to clone the solution accelerator repo into your workspace. Once the repo is cloned into your workspace, please execute the **RUNME** notebook in the repo in order to create the cluster and job you can use to run the notebooks.