Brain Architecture Project

Data and Code for the Developing Human Brain

Resources for our Cell Detection and Data for the Human Developing Brain

Datasets Available

• 13GW Visualize
• 23GW Visualize

Available Code

• Proposed Algorithm Link to Github
• Model_1 (MEDIAR) Code Link to Github
• Model_2 (Multistream Cell Segmentation) Code Link to Github
• Repo for Evaluation and Colab notebooks to run the above codes Link to Github
• Registration Link to GitHub

Data Samples for Cell Detection

• Training Data Tiles Centers
• Test Data Tiles Ground-truth
• Detected Centers Proposed Model 1 Model 2

Publications

• Partha Mitra, Jaikishan Jayakumar, Mohanasankar Sivaprakasam et al. A three-dimensional histological cell atlas of the developing human brain, 10 January 2025, PREPRINT (Version 1) available at Research Square. Link
• Lee, G., Kim, S., Kim, J. & Yun, S. (2023). MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy. Proceedings of The Cell Segmentation Challenge in Multi-modality High-Resolution Microscopy Images, in Proceedings of Machine Learning Research 212:1-16. Available from Link.
• Lou, W., Yu, X., Liu, C., Wan, X., Li, G., Liu, S., & Li, H. (2023). Multi-stream Cell Segmentation with Low-level Cues for Multi-modality Images. Proceedings of The Cell Segmentation Challenge in Multi-modality High-Resolution Microscopy Images, in Proceedings of Machine Learning Research 212:1-10. Available from Link.
• Ma, J., Xie, R., Ayyadhury, S. et al. The multimodality cell segmentation challenge: toward universal solutions. Nat Methods 21, 1103–1113 (2024). Link.