Published October 11, 2023
| Version v2
Other
Open
PlantSeg Plant Nuclei 3D UNet
Description
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
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. Patch size for this model during inference can be flexible. (Uploaded via https://bioimage.io)
Files
cover.png
Files
(12.4 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:4287511376928bd1e4db26c619c8600c
|
92.1 kB | Preview Download |
|
md5:d54a77d27eef446fbb12c8c0d4141d83
|
127 Bytes | Download |
|
md5:bafc60ccea985ae773db3244e36983cf
|
390 Bytes | Preview Download |
|
md5:7c83faed4a8fed8713ac818e617f5e63
|
4.1 MB | Download |
|
md5:844cdeacddd36806deae363dc3ac505c
|
40.9 kB | Preview Download |
|
md5:0680e09505ad43abfda26b168e7ca753
|
115.4 kB | Preview Download |
|
md5:931ee128dac5e13cf8c1f3600e5c971e
|
100.3 kB | Preview Download |
|
md5:88efe07746dbbf682e4b533fe1380408
|
2.3 kB | Download |
|
md5:a929d27ece189dd9f4025ad3c1b344d3
|
884.9 kB | Download |
|
md5:53328f5196bea6e331cc5cb8ae03dc14
|
7.1 MB | Download |
