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nucount
fabda/nucount
nucount is a image segmentation model from fabda. Use it for the image segmentation task on the model card, and read the license before you ship it in a product. It is set up for transformers. The card lists the license as gpl-3.0.
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At a glance
- Task
- Image Segmentation
- Library
- transformers
- License
- gpl-3.0
- Access
- Public
- Created
- Mar 1, 2023
- Updated
- Mar 3, 2023
- SHA
- c30b8f1b
Spaces
Model card
From the Hugging Face model README
3DL_NuCount model
Model author: Fabrice Daian
Model description
3DL_NuCount model has been designed by fine tuning a pretrained Stardist3D model [1,2] using a home made dataset [3] in order to assess the number of cells present in a given 3D image stack acquired using an optical microscope. Training and Inference Notebooks are hosted on our Github repo [4].
Stardist Training parameters
- patch size: (48,96,96)
- batch size: 32
- epochs : 100
- data augmentation : flip/rotation/intensity
- image normalization: normalize channel independantly
- anisotropy: empirical
- rays : 96
Training dataset parameters
- tile size : (4,63,128,128)
- split : Train 0.8 / Val 0.2
Inference
- patch size : (784,784,:)
- image size : (2048,2048,:)
- model name : weights_best_1.h5
- config file : config.json
- threshold file : thresholds.json
References
- Task
- Image Segmentation
- Library
- transformers
- License
- gpl-3.0
- Languages
- en
- Created
- Mar 1, 2023
- Updated
- Mar 3, 2023