Ecosyste.ms: Issues

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GitHub / stardist/stardist issues and pull requests

#291 - StarDist is not running on python 3.12

Issue - State: open - Opened by emir-radkevich 18 days ago
Labels: bug

#288 - TypeError: argument 1 must be numpy.ndarray, not numpy.ndarray

Issue - State: open - Opened by Yifan-debug about 2 months ago - 1 comment
Labels: bug

#287 - Error while trying to load model

Issue - State: open - Opened by Teranis 2 months ago
Labels: bug

#286 - stardist 3d large loading on the fly , unknow error

Issue - State: open - Opened by Nal44 3 months ago - 1 comment

#285 - stardist: config file doesn't exist

Issue - State: closed - Opened by GBeattie 3 months ago - 2 comments
Labels: bug

#281 - Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows

Pull Request - State: open - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#280 - ValueError: axes (YXC) must be of length 2

Issue - State: closed - Opened by Rafael-Silva-Oliveira 5 months ago - 2 comments
Labels: bug

#279 - Url for QuPath plugin broken

Issue - State: closed - Opened by camilla31 5 months ago - 2 comments
Labels: bug

#278 - Fix render_label

Pull Request - State: closed - Opened by bentaculum 7 months ago - 2 comments

#277 - Inefficient order of intersection checks during 3D NMS ?

Issue - State: open - Opened by jules-vanaret 7 months ago - 8 comments
Labels: bug

#276 - export_bioimageio not working with the new biomageio.core library

Issue - State: open - Opened by esgomezm 7 months ago - 7 comments

#275 - larger nuclei not detected

Issue - State: closed - Opened by me-nobody 7 months ago - 9 comments
Labels: bug

#274 - The segmentation results with the same StarDist2D are different on different machines

Issue - State: closed - Opened by ccalafiore 7 months ago - 13 comments
Labels: bug

#273 - Add seed option to random_label_cmap

Pull Request - State: closed - Opened by hwarden162 7 months ago - 7 comments

#272 - `render_label()` not working with matplotlib 3.9.x

Issue - State: closed - Opened by ktpolanski 9 months ago - 2 comments
Labels: bug

#271 - Error while saving output file using stardist-predict2d.py

Issue - State: open - Opened by migueLib 9 months ago - 2 comments
Labels: bug

#270 - Fix PyPI test workflow

Pull Request - State: closed - Opened by uschmidt83 9 months ago

#269 - Refactor wheel building workflow

Pull Request - State: closed - Opened by uschmidt83 9 months ago

#268 - Changes for 0.9.0 release

Pull Request - State: closed - Opened by uschmidt83 9 months ago

#267 - Refactor GitHub action workflows

Pull Request - State: closed - Opened by uschmidt83 9 months ago

#266 - Add support for Keras 3

Pull Request - State: closed - Opened by uschmidt83 10 months ago - 1 comment

#265 - Update utils.py

Pull Request - State: closed - Opened by juliancstrocodes 10 months ago - 1 comment

#264 - Cannot run a training because of the name

Issue - State: closed - Opened by I-Guy 10 months ago - 2 comments
Labels: bug

#263 - Add notebooks for training with sparse annotation

Pull Request - State: open - Opened by ksugar about 1 year ago

#262 - ImportError for stardist

Issue - State: open - Opened by hliu56 about 1 year ago - 1 comment
Labels: bug

#261 - Is a bug or misunderstanding the source code?

Issue - State: closed - Opened by mmlyj about 1 year ago
Labels: bug

#260 - Overflow error :int too big to convert

Issue - State: open - Opened by AngelosDid about 1 year ago - 1 comment
Labels: bug

#259 - Add stardist to Bioconda

Issue - State: open - Opened by migueLib about 1 year ago - 5 comments

#258 - Receptive field measure improvement

Issue - State: closed - Opened by etasnadi about 1 year ago - 1 comment

#255 - Added .groovy to export qupath annotations for stardist multiclass

Pull Request - State: open - Opened by Nikdenof over 1 year ago

#254 - Fix and improve the export function for Bioimage.IO

Pull Request - State: closed - Opened by qin-yu over 1 year ago - 10 comments

#252 - `export_bioimageio()` causes config file error

Issue - State: closed - Opened by qin-yu over 1 year ago - 4 comments
Labels: bug

#251 - Tensforflow to pytorch migration

Issue - State: open - Opened by manerotoni over 1 year ago - 1 comment

#250 - Using `stardist-conic` without `pip install`

Issue - State: open - Opened by ajinkya-kulkarni over 1 year ago - 6 comments

#249 - Resolve integer overflow when running on a large 3D image

Pull Request - State: closed - Opened by ximion over 1 year ago - 1 comment

#248 - Update Qhull

Pull Request - State: open - Opened by ximion over 1 year ago - 4 comments

#247 - Details about pre-trained 2D_versatile_he model

Issue - State: open - Opened by Minstrellee over 1 year ago

#246 - Cannot customize the `augmenter` in 2D training?

Issue - State: closed - Opened by ajinkya-kulkarni over 1 year ago - 2 comments

#245 - FIJI crashes when trying to process my 32kx32k stitched dapi-stained nuclei TIF

Issue - State: open - Opened by kitovyj over 1 year ago - 1 comment
Labels: bug

#244 - Fix `sdist` building

Pull Request - State: closed - Opened by uschmidt83 over 1 year ago

#242 - Fix wheel building

Pull Request - State: closed - Opened by uschmidt83 over 1 year ago

#241 - Stardist import fails in fresh installation (tensorflow.keras has no attribute __version__)

Issue - State: closed - Opened by constantinpape over 1 year ago - 7 comments
Labels: bug

#240 - Changes for 0.8.4 release

Pull Request - State: closed - Opened by uschmidt83 over 1 year ago

#239 - Fiji crashing upon running trained Stardist model on Mac M1

Issue - State: open - Opened by rasoolkp over 1 year ago
Labels: bug

#238 - Macbook M2 failed to model3d.train with 'GPU'

Issue - State: open - Opened by blancfrederic over 1 year ago - 2 comments
Labels: bug

#237 - Replaced `from tqdm import tqdm` with `from tqdm.auto import tqdm`

Pull Request - State: open - Opened by ajinkya-kulkarni over 1 year ago - 6 comments

#236 - Crashing when loading pretrained models

Issue - State: closed - Opened by sckaff over 1 year ago - 1 comment
Labels: bug

#235 - Crashes when running predict_instances on a 3D image

Issue - State: closed - Opened by ximion over 1 year ago - 6 comments
Labels: bug

#234 - Conic 2022

Pull Request - State: closed - Opened by ukanwat over 1 year ago

#233 - Problem with output segmentation with 2D_versatile_he

Issue - State: open - Opened by niccolo99mandelli over 1 year ago - 1 comment
Labels: bug

#232 - Conic 2022

Pull Request - State: closed - Opened by ukanwat over 1 year ago

#230 - Updated README.md

Pull Request - State: closed - Opened by ajinkya-kulkarni almost 2 years ago - 1 comment

#229 - Layer or Model in invalid state TF 2.12 - bioimageio export - _compute_receptive_field

Issue - State: open - Opened by esgomezm almost 2 years ago - 6 comments
Labels: bug

#228 - DNN library is not found.

Issue - State: open - Opened by ShangWeiKuo almost 2 years ago - 2 comments
Labels: bug

#227 - Support for Python 3.11

Issue - State: closed - Opened by fluffygreenpillow almost 2 years ago - 6 comments

#226 - An error in 2D_versatile_he

Issue - State: closed - Opened by HectorTo almost 2 years ago - 20 comments

#225 - Planned release of the 3D pretrained model?

Issue - State: closed - Opened by ajinkya-kulkarni almost 2 years ago - 1 comment

#224 - Cannot suppress output of model.predict_instances(...)

Issue - State: closed - Opened by ajinkya-kulkarni almost 2 years ago - 4 comments
Labels: enhancement

#223 - Fix memory leak in stardist2d NMS

Pull Request - State: open - Opened by ashajkofci almost 2 years ago - 1 comment

#222 - `use_gpu` flag not working as expected

Issue - State: closed - Opened by zoccoler almost 2 years ago - 3 comments
Labels: bug

#221 - Updated `README.md` for the latest version of Fiji

Pull Request - State: closed - Opened by ajinkya-kulkarni almost 2 years ago - 1 comment

#220 - Binary mask

Issue - State: closed - Opened by abehzadnia almost 2 years ago - 1 comment

#219 - Fix compilation issue on Windows

Pull Request - State: closed - Opened by uschmidt83 almost 2 years ago

#218 - README inference example fail on M1 macbook after fresh install

Issue - State: open - Opened by bgriffen almost 2 years ago - 2 comments
Labels: bug

#217 - Pytorch implementation

Issue - State: closed - Opened by AjinkyaDeshpande39 about 2 years ago - 1 comment

#216 - Cannot apply EarlyStopping function to StarDist2D.train

Issue - State: closed - Opened by ShangWeiKuo about 2 years ago - 1 comment

#215 - Coordinates of labelled cell/objects

Issue - State: closed - Opened by Erfanahmed84 about 2 years ago - 1 comment

#214 - How to predict with GPU

Issue - State: closed - Opened by yevgeniyclaudio about 2 years ago - 4 comments
Labels: bug

#213 - For the arm64 M1 in README, stress Monterey (macOS 12)

Pull Request - State: closed - Opened by psobolewskiPhD over 2 years ago - 2 comments

#212 - ModuleNotFoundError: No module named 'stardist.lib.stardist2d'

Issue - State: closed - Opened by lanfz2000 over 2 years ago - 1 comment
Labels: bug

#211 - Pyodide version.

Issue - State: open - Opened by Mmasoud1 over 2 years ago - 1 comment

#210 - how to get the average precision

Issue - State: closed - Opened by wzr0108 over 2 years ago - 1 comment

#209 - adapt to list of test summaries

Pull Request - State: closed - Opened by FynnBe over 2 years ago

#208 - TensorFlow check failed for large images

Issue - State: closed - Opened by agclark12 over 2 years ago - 2 comments
Labels: bug

#207 - ValueError

Issue - State: closed - Opened by WXY-Belief over 2 years ago - 1 comment
Labels: bug

#206 - How to interpret stardist.matching results?

Issue - State: closed - Opened by fangpingmu over 2 years ago - 1 comment
Labels: bug

#205 - Error when importing stardist on macOS 10.13

Issue - State: closed - Opened by ElpadoCan over 2 years ago - 5 comments
Labels: bug

#204 - stardist-predict3D ignores values for nms and prob thresholds

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

#203 - How did you create the MASK images?

Issue - State: closed - Opened by ghezalahmad over 2 years ago - 1 comment

#202 - Different results from Python Stardist and FIJI

Issue - State: closed - Opened by lambda-science over 2 years ago - 1 comment

#201 - Scripts

Pull Request - State: closed - Opened by maweigert over 2 years ago

#200 - Add prediction generators

Pull Request - State: closed - Opened by uschmidt83 over 2 years ago

#199 - Need of prediction mask

Issue - State: open - Opened by jtyytim over 2 years ago - 7 comments

#198 - Update macOS M1 install instructions in README

Pull Request - State: closed - Opened by psobolewskiPhD over 2 years ago - 3 comments

#197 - Questions about the training data set

Issue - State: closed - Opened by maxi2015qwe over 2 years ago - 1 comment

#196 - retrain model with curated images advice ?

Issue - State: closed - Opened by Nal44 over 2 years ago - 1 comment

#195 - NMS start suppressing crashes

Issue - State: open - Opened by usmanqureshi94 over 2 years ago - 7 comments
Labels: bug

#194 - Segmentation of highly crowded images

Issue - State: open - Opened by SarkkinenJ almost 3 years ago - 1 comment

#193 - StarDist beyond bioimaging

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

#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