PlantSeg Plant Nuclei 3D UNet

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. Patch size for this model during inference can be flexible. (Uploaded via https://bioimage.io)

Download RDF Package This is a PlantSeg model (or a pytorch-3dunet 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 StarDist (or CSBDeep) model is also available on Bioimage.IO at https://bioimage.io/#/?id=10.5281%2Fzenodo.8421755

Keywords

bioimage.io:model, ovules, segmentation, boundary-segmentation, instance-segmentation, bioimage.io, plant, plantseg, nucleus-segmentation, confocal-microscopy, nuclei, pytorch, unet, to-pro-3, 3d

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