A curated list of awesome Bioimage Analysis Challenges. The goal of this list is to be a place where Bioimage Analysis Developers can find challenges to evaluate and benchmark their algorithms. In order to be added the linked challenge should have:

• imaging data available for public download
• a specified image analysis task (e.g. segmentation, classification)
• a metric for evaluating performance
• some form of "annotation", "labeling", or "ground truth"

This is list currently organized by scientific domain.

• Awesome Bioimage Analysis Challenges
  • Cell Biology
  • CryoEM
  • Neuroscience
  • Pathology

Challenges for cell biology data

• ISBI Cell Tracking - Segment and track moving cells in time-lapse video sequences.
• Kaggle Data Science Bowl 2018 - Segement nuclei across varied conditions.
• Kaggle HPA - Classify mixed patterns of proteins in microscope images from the human protein atlas.

Challenges for Cryo EM and Cryo ET data

• SHREC 2021 - Localization and classification of biological particles in simulated cryo-electron tomograms.

Challenges for neuroscience data

• Neurofinder - Cell segmentation for 2-photon caclium imaging in mice with manually labeled ground truth.

Challenges for pathology data

• Camelyon17 - Automated detection and classification of breast cancer metastases in whole-slide histology images