stardist/stardist issues and pull requests

#192 - Proposition to add Cytomine to "Plugins for other software".

Pull Request - State: open - Opened by PaulBarZa almost 3 years ago

#191 - command line --n_tiles

Issue - State: closed - Opened by romainGuiet almost 3 years ago - 6 comments
Labels: bug

#190 - Threshold optimization step in 2D pipeline after training error

Issue - State: closed - Opened by Nal44 almost 3 years ago - 10 comments

#189 - Improve packaging and deployment workflow

Pull Request - State: closed - Opened by uschmidt83 almost 3 years ago

#188 - problem many labels on predicted 3D image

Issue - State: open - Opened by rprisca almost 3 years ago - 3 comments

#187 - Add the bioimageio resource description to deserialized stardist model

Pull Request - State: closed - Opened by constantinpape almost 3 years ago - 16 comments

#186 - Update cibuildwheel config

Pull Request - State: closed - Opened by uschmidt83 almost 3 years ago

#185 - Update Labkit labeling instructions

Issue - State: closed - Opened by Theresa-S almost 3 years ago - 1 comment

#184 - Pending changes for 0.8.0 release

Pull Request - State: closed - Opened by uschmidt83 almost 3 years ago - 1 comment

#183 - Fix failing tests

Pull Request - State: closed - Opened by uschmidt83 almost 3 years ago

#182 - Problem when running 3D model on 2-channel stack

Issue - State: open - Opened by lcferme about 3 years ago - 6 comments

#181 - Add optional scaling preprocessing to prediction

Pull Request - State: closed - Opened by maweigert about 3 years ago

#180 - h5py requirement of stardist v0.7.3 not compatible with tensorflow >2.5

Issue - State: open - Opened by ElpadoCan about 3 years ago - 8 comments
Labels: bug

#179 - 3D StarDist for LC-OCT images

Issue - State: open - Opened by Optimox about 3 years ago - 2 comments

#178 - problem to save a predicted big 3d image

Issue - State: closed - Opened by rprisca about 3 years ago - 2 comments

#177 - changes nargs from 2 to 3 for n_tiles

Pull Request - State: closed - Opened by romainGuiet about 3 years ago - 1 comment

#176 - example of training MoNuSeg2018 dataset?

Issue - State: closed - Opened by zhangliukun about 3 years ago - 1 comment

#175 - StarDist3D memory usage depends on total dataset size and not on `train_patch_size` and `train_batch_size`

Issue - State: closed - Opened by aarpon about 3 years ago - 5 comments
Labels: bug

#174 - Predictions are cut off for larger images on Apple M1/macOS11/tensorflow-metal 2.6

Issue - State: open - Opened by maweigert about 3 years ago - 6 comments
Labels: bug

#173 - minor docstring fix

Pull Request - State: closed - Opened by kevinyamauchi about 3 years ago - 1 comment

#172 - Train stardist using ImageDataGenerator

Issue - State: closed - Opened by LuisFMCuriel about 3 years ago - 1 comment

#171 - Use bioimageio.core.build_spec to generate stardist export

Pull Request - State: closed - Opened by constantinpape over 3 years ago - 64 comments

#170 - Image scale / resolution and size

Issue - State: closed - Opened by lstrgar over 3 years ago - 2 comments

#169 - libstardist3D C++ implementation for 3D prediction?

Issue - State: closed - Opened by tractatus over 3 years ago - 1 comment

#168 - 255 labels

Issue - State: closed - Opened by usmanqureshi94 over 3 years ago - 5 comments

#167 - model.predict crashes on colab for 3D data

Issue - State: closed - Opened by kapoorlab over 3 years ago - 1 comment

#166 - Windows 10 - StarDist-V073 - save_weights requires h5py when saving in hdf5

Issue - State: closed - Opened by cberri over 3 years ago - 12 comments
Labels: bug

#165 - about annotations for multi-label classification

Issue - State: closed - Opened by captainst over 3 years ago - 1 comment

#164 - the formula to calculate AP (para.3.2 in the paper)

Issue - State: closed - Opened by captainst over 3 years ago - 2 comments

#163 - relabel_image_stardist for empty image errors out

Issue - State: closed - Opened by maweigert over 3 years ago - 2 comments
Labels: bug

#162 - Can't call from_pretrained inside a multiprocessing worker

Issue - State: closed - Opened by kesinger over 3 years ago - 3 comments
Labels: bug

#161 - Generalization capabilities of trained models

Issue - State: closed - Opened by anorak94 over 3 years ago - 1 comment

#160 - Should be Train_steps_per_epoch changed according to training set size and batch size?

Issue - State: closed - Opened by javierpastorfernandez over 3 years ago - 3 comments

#159 - Move matching.py to an independent package

Issue - State: open - Opened by tibuch over 3 years ago - 1 comment

#158 - Exporting Models to Use on Other Platforms

Issue - State: closed - Opened by michaelschwimmer over 3 years ago - 1 comment

#157 - Include matplotlib.pyplot in example code block

Pull Request - State: closed - Opened by psobolewskiPhD over 3 years ago - 1 comment

#156 - Unpin numpy version in pyproject.toml

Issue - State: closed - Opened by weinberz over 3 years ago - 7 comments
Labels: bug

#155 - Undefined variable dist

Issue - State: closed - Opened by frycaktadeas over 3 years ago - 1 comment
Labels: bug

#154 - Predicting completed shapes for partially visible cells at the image boundary gives error

Issue - State: closed - Opened by qinghongwan over 3 years ago - 2 comments
Labels: bug

#153 - Memory Error during training

Issue - State: closed - Opened by Optimox over 3 years ago - 9 comments

#152 - it seems that python 3.8 doesn't work

Issue - State: closed - Opened by maxi2015qwe over 3 years ago - 3 comments

#151 - Is there a way to limit the cores dedicated to prediction process?

Issue - State: closed - Opened by pouyadfd over 3 years ago - 2 comments

#149 - Bioimageio modelzoo export

Pull Request - State: closed - Opened by maweigert over 3 years ago

#148 - False positive prediction at Image border

Issue - State: closed - Opened by codingS3b over 3 years ago - 3 comments

#146 - Additional Training Performance

Issue - State: closed - Opened by william-silversmith over 3 years ago - 3 comments

#143 - Version of numpy that satisfies tensorflow and gputools?

Issue - State: closed - Opened by Cocomolch4000 over 3 years ago - 3 comments

#140 - How to deal with overlapping labels?

Issue - State: closed - Opened by Cocomolch4000 almost 4 years ago - 6 comments

#139 - Stardist seems not to work with python 3.9

Issue - State: closed - Opened by Cocomolch4000 almost 4 years ago - 8 comments

#138 - The results I got are very different from those in the paper

Issue - State: closed - Opened by f-thirty almost 4 years ago - 10 comments

#137 - Personalized Augmentation Method

Issue - State: closed - Opened by javierpastorfernandez almost 4 years ago - 6 comments

#136 - A question of evaluation

Issue - State: open - Opened by jtyytim almost 4 years ago - 6 comments

#134 - Further Training of a Completed StarDist 3D Model

Issue - State: closed - Opened by michaelschwimmer almost 4 years ago - 1 comment

#130 - 3D prediction memory leak?

Issue - State: closed - Opened by Optimox almost 4 years ago - 3 comments

#126 - Support transfer learning

Issue - State: open - Opened by uschmidt83 almost 4 years ago - 2 comments
Labels: enhancement

#110 - Question: Best practice to change Model Backbone and other core changes in the stardist2D?

Issue - State: closed - Opened by caprioGirl about 4 years ago - 3 comments

#93 - loading 2D_versatile_fluo error

Issue - State: open - Opened by Marckobudo over 4 years ago - 6 comments

#68 - 'StarDist2D' object has no attribute '_tile_overlap'

Issue - State: open - Opened by nuh-sikander over 4 years ago - 32 comments

#57 - Data generator for large datasets

Issue - State: closed - Opened by nalinratnayeke over 4 years ago - 12 comments

#48 - SSLCertVerificationError when trying to use versatile pretrained model

Issue - State: closed - Opened by imagejan almost 5 years ago - 5 comments

#37 - Export imageJ ROIs for 3D polyhedra

Issue - State: closed - Opened by michaelschwimmer almost 5 years ago - 9 comments

GitHub / stardist/stardist issues and pull requests