Published December 19, 2023
| Version 0.1.0
Model
Open
StarDist Model for Nuclei Segmentation in Developing Tribolium Castaneum Embryo Images
Description
This StarDist model has been specifically fine-tuned for nuclei segmentation in images of Developing Tribolium Castaneum embryos, provided by Dr. A. Jain from the Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany. The model addresses the unique challenges presented by the 3D dataset from the Cell Tracking Challenge, which has been adapted to a 2D format for this purpose.
- Dataset: Cell Tracking Challenge 3D Datasets
The ZeroCostDL4Mic notebook used for fine-tuning is the StarDist in 2D.
- Fine-Tuning Notebook: StarDist ZeroCostDL4Mic Notebook
Files
doc.md
Files
(193.1 MB)
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Additional details
References
- von Chamier, L., Laine, R. F., Jukkala, J., Spahn, C., Krentzel, D., Nehme, E., ... & Henriques, R. (2021). Democratising deep learning for microscopy with ZeroCostDL4Mic. Nature communications, 12(1), 2276.
- Schmidt, U., Weigert, M., Broaddus, C., & Myers, G. (2018). Cell detection with star-convex polygons. In Medical Image Computing and Computer Assisted Intervention–MICCAI 2018: 21st International Conference, Granada, Spain, September 16-20, 2018, Proceedings, Part II 11 (pp. 265-273). Springer International Publishing