Published October 11, 2023 | Version v4
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StarDist Plant Nuclei 3D ResNet

Creators

  • 1. EMBL

Description

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This is a StarDist model (or a CSBDeep model) for segmenting plant nuclei in 3D images. Trained by Qin Yu from Kreshuk Lab at EMBL with training datasets from Schneitz Lab at TUM. A PlantSeg (or pytorch-3dunet) model is also available on Bioimage.IO at https://bioimage.io/#/?id=10.5281%2Fzenodo.8401064

 

Notes

This widely applicable model is trained for 3D nuclei instance segmentation and with 3D nuclei images of Arabidopsis ovules with TO-PRO-3 stain. TO-PRO-3 nuclei stain detects double-stranded nucleic acids and hence can be a useful tool for nuclear DNA quantification and 3D volumetric nuclei extraction. This model is trained with dataset 1136, 1137, 1139, 1170 and validated with 1135. (Uploaded via https://bioimage.io)

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