/master_thesis_code

Primary LanguagePythonMIT LicenseMIT

Code Repository for Master's Thesis

K-POP: Predicting Distance to Focal Plane for Kato-Katz Prepared Microscopy Slides Using Deep Learning

This repository contains all code produced to write my master's thesis available here.

The model code which is integrated as a git submodule is hosted on HuggingFace.

To fully initialize all submodules run the following after cloning:

git submodule update --init --recursive

The machine learning pipeline works as follows:

  1. Using the code in annotation-preprocessing metadata and images are extracted from a database. The data is prepared to be usable by the tool Focus Annotator.
  2. Data is annotated using Focus Annotator (folder: focus_annotator)
  3. Annotations are post processed to csv format to be easier to load with pandas (folder: data-preprocessing).
  4. The models are trained and evaluated in models.