HenriquesLab / HenriquesLab/ZeroCostDL4Mic
.h5 file format for 3D UNET
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- Dominant language
- Jupyter Notebook
- Stars
- 652
- Forks
- 144
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Description
Hello,
I have been using the 3D unet notebook locally and the results have been fantastic!
I have a small suggestion to make. I have been annotating my training datasets with the "Carving" tool in Ilastik and have been exporting segmented data in the .h5 file formats. Would it be possible to implement something in the training part (section 3.1) of the 3d-Unet notebook so that it can recognize .h5 file formats?
Thank you once again!
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the 3D UNET notebook and inspect the training code in section 3.1, focusing on how dataset files are currently discovered and loaded. Compare that path with the .h5 files exported by Ilastik. Done means the training section recognizes and uses the requested .h5 format without breaking the existing workflow.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- machine-learning
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100