HenriquesLab/ZeroCostDL4Mic

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ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy

Stars: 652
Forks: 144
Open beginner issues: 0
Indexed issues: 53

Dominant language: Jupyter Notebook
License: MIT
Last GitHub push: Sep 15, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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53 open issues indexed

Quality Control notebook Install dependencies error Open

Difficulty 3/5 1-2 days Newbie friendliness 32/100

HenriquesLab/ZeroCostDL4Mic#351 · Opened Aug 12, 2025
Deep-STORM_2D_ZeroCostDL4Mic Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

HenriquesLab/ZeroCostDL4Mic#350 · Opened Jul 18, 2025
ImportError: numpy.core.multiarray failed to import` / `AttributeError: _ARRAY_API not found` when importing stardist Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

HenriquesLab/ZeroCostDL4Mic#348 · 1 comment · Opened Jun 4, 2025
StarDist_2D Load key dependencies issue Open

Difficulty 3/5 1-2 days Newbie friendliness 20/100

HenriquesLab/ZeroCostDL4Mic#347 · 1 comment · Opened Apr 30, 2025
ImportError: multi.core.array failed to import Open

dependencies

Difficulty 4/5 3-5 days Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#346 · 2 comments · Opened Mar 31, 2025
UNET 3D,old model can not use in new version Open

dependencies

Difficulty 4/5 3-5 days Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#345 · 1 comment · Opened Mar 28, 2025
ImportError: `imsave` Removed from `tifffile` – Update Notebook to Use `imwrite` Open

dependencies

HenriquesLab/ZeroCostDL4Mic#343 · 1 comment · 1 assignee · Opened Mar 5, 2025
DEEPSTORM GOOGLE COLAB - issue with training the model Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#342 · Opened Feb 11, 2025
StarDist2D path issue: models are not stored in the user defined location Open

HenriquesLab/ZeroCostDL4Mic#340 · 2 comments · 1 assignee · Opened Jan 27, 2025
StarDist_3D_ZeroCostDL4Mic notebook issue installing dependencies Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#337 · 1 comment · Opened Nov 8, 2024
Splinedist failing to install dependencies Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

HenriquesLab/ZeroCostDL4Mic#328 · Opened Sep 24, 2024
Failed to train UNET Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#324 · 7 comments · Opened Aug 26, 2024
fnet_3D | Failed to build scikit-learn Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

HenriquesLab/ZeroCostDL4Mic#323 · Opened Aug 9, 2024
Cellpose - two models not found Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#321 · 1 comment · Opened Jul 29, 2024
issue with stardist2D prediction progresss Open

HenriquesLab/ZeroCostDL4Mic#318 · 1 comment · 1 assignee · Opened Apr 16, 2024
Where to find the requirement file to create a local env Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

HenriquesLab/ZeroCostDL4Mic#316 · 1 comment · Opened Apr 8, 2024
Cellpose 2 - Evaluate your model and generate predictions issues Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#314 · Opened Mar 31, 2024
Issue saving simulated data in Deep-STORM notebook. Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

HenriquesLab/ZeroCostDL4Mic#311 · Opened Feb 23, 2024
EmpedSeg: requested version for torch and torchvision not found, with different versions type error while training Open

bug dependencies

HenriquesLab/ZeroCostDL4Mic#306 · 2 comments · 1 assignee · Opened Jan 17, 2024
3D unet: Problem with Section 5.4, cannot download model as bioImage Open

HenriquesLab/ZeroCostDL4Mic#288 · 8 comments · 1 assignee · Opened Aug 29, 2023
ModuleNotFoundError: No module named 'splinegenerator' Open

Difficulty 2/5 1-3 hours Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#273 · 3 comments · Opened Jun 5, 2023
[Feature] Full notebook CI testing Open

HenriquesLab/ZeroCostDL4Mic#271 · 2 comments · 1 assignee · Opened Jun 2, 2023
Unable to use the TF_SavedModel in Stardist 2D plugin in Fiji Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

HenriquesLab/ZeroCostDL4Mic#269 · 2 comments · Opened Jun 2, 2023
2D Stardist keeps crashing when Generating prediction(s) from unseen dataset Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#265 · 1 comment · Opened May 4, 2023
Stardist 2D prediction error output , 1000*1000 with 16bit Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#257 · 1 comment · Opened Apr 1, 2023
Error in 1.3. Load key dependencies StarDist_2D Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

HenriquesLab/ZeroCostDL4Mic#249 · 10 comments · Opened Mar 14, 2023
YOLOv2 section 1.3 tensorflow Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

HenriquesLab/ZeroCostDL4Mic#246 · 2 comments · 1 reaction · Opened Feb 27, 2023
Stardist error message when running multiple images in google drive Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

HenriquesLab/ZeroCostDL4Mic#237 · 1 comment · Opened Feb 2, 2023
StarDist_3D image artifact issue Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

HenriquesLab/ZeroCostDL4Mic#235 · 7 comments · Opened Jan 12, 2023
Training issues Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

HenriquesLab/ZeroCostDL4Mic#218 · 5 comments · Opened Oct 27, 2022
Training failed after data augmentation Open

Difficulty 4/5 3-5 days Newbie friendliness 15/100

HenriquesLab/ZeroCostDL4Mic#215 · 5 comments · Opened Oct 14, 2022
DFCAN 3D Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#209 · 3 comments · Opened Sep 10, 2022
Yolov2 fails at 1.3 Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#208 · 1 comment · 1 reaction · Opened Sep 8, 2022
Label-free prediction (fnet) 2D error when setting training parameters Open

HenriquesLab/ZeroCostDL4Mic#192 · 6 comments · 1 assignee · Opened May 19, 2022
YOLOv2 Step 6 fails with error ValueError: axes don't match array Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

HenriquesLab/ZeroCostDL4Mic#186 · 1 reaction · Opened Apr 22, 2022
How to convert annotation - json format to pascal voc xml file for YoloV2 Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#182 · 6 comments · Opened Mar 25, 2022
Cellpose training Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

HenriquesLab/ZeroCostDL4Mic#179 · 10 comments · Opened Mar 11, 2022
Mask RCNN model shape error while generating prediction from unseen dataset Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#176 · 1 comment · Opened Mar 7, 2022
Running the script on a local runtime produces errors in loading key dependencies Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

HenriquesLab/ZeroCostDL4Mic#171 · 2 comments · Opened Feb 22, 2022
In Stardist2D number_of_steps is calculated assuming all training data has the same size Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

HenriquesLab/ZeroCostDL4Mic#167 · 2 comments · Opened Feb 9, 2022
Error: StarDist_2D keeps disconnecting runtime in the middle of the run Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#166 · 1 comment · Opened Feb 4, 2022
Error when creating data sets, issues when training large images and prediction output format Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#156 · 3 comments · Opened Nov 28, 2021
YOLOv2 notebook local error - section 4.1 Open

Local notebook

Difficulty 3/5 1-2 days Newbie friendliness 35/100

HenriquesLab/ZeroCostDL4Mic#152 · 1 comment · Opened Nov 8, 2021
Invalid distribution --Stardist (-tardist) Open

Local notebook

Difficulty 3/5 1-2 days Newbie friendliness 35/100

HenriquesLab/ZeroCostDL4Mic#145 · Opened Oct 18, 2021
StarDist notebook local error Open

Local notebook

Difficulty 1/5 Under an hour Newbie friendliness 55/100

HenriquesLab/ZeroCostDL4Mic#144 · 1 comment · Opened Oct 18, 2021
U-Net 2D Quality Control Error with .png test images Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

HenriquesLab/ZeroCostDL4Mic#143 · 3 comments · Opened Oct 12, 2021
Training models to identify multiple organelles with 3D UNET Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

HenriquesLab/ZeroCostDL4Mic#142 · 2 comments · Opened Oct 11, 2021
Crash when trying to run RetinaNet Open

HenriquesLab/ZeroCostDL4Mic#140 · 7 comments · 1 assignee · Opened Sep 6, 2021
Errors when running YOLO notebook while connected to a local runtime Open

Local notebook

Difficulty 4/5 3-5 days Newbie friendliness 30/100

HenriquesLab/ZeroCostDL4Mic#139 · 4 comments · Opened Sep 2, 2021
.h5 file format for 3D UNET Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

HenriquesLab/ZeroCostDL4Mic#116 · 1 comment · Opened Jul 6, 2021

HenriquesLab/ZeroCostDL4Mic

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