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HenriquesLab

6 indexed repositories · View on GitHub

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

Jupyter Notebook · 652 stars
NanoPyx
Nanoscopy library for Python (NanoPyx, the successor to NanoJ) - focused on light microscopy and super-resolution imaging

Jupyter Notebook · 93 stars
DL4MicEverywhere
Bringing the ZeroCostDL4Mic experience running everywhere via easy-to-install docker images

Jupyter Notebook · 87 stars
rxiv-maker
Rxiv-Maker is a GitHub-native framework that converts markdown into a publication-ready PDF. It automates scientific preprint generation ...

Python · 40 stars
EZInput
EZInput is a Python library that simplifies the creation of graphical user interfaces (GUIs) both in the terminal and in Jupyter notebook...

Python · 4 stars
VLab4Mic

Python · 3 stars

Beginner friendly Everything

Open All

eature request: automatically continue long figure legends on the next page Open

Difficulty 5/5 Over a week Newbie friendliness 38/100

HenriquesLab/rxiv-maker#324 · 1 comment · Opened Aug 11, 2026
random_seed not propagated to randomise_axial_position (dormant reproducibility gap) Open

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

HenriquesLab/VLab4Mic#135 · Opened Jun 9, 2026
Major Issues with nanopyx.methods.esrrf.parameter_sweep Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

HenriquesLab/NanoPyx#153 · 2 comments · Opened Jun 8, 2026
Unable to Implement Workflow Class due to functions lacking attribute '_run_types' Open

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

HenriquesLab/NanoPyx#152 · 2 comments · Opened Jun 4, 2026
Differences from magicgui? Open

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

HenriquesLab/EZInput#8 · 2 comments · Opened Mar 17, 2026
Was the registration operation used when calculate error_map ? Open

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

HenriquesLab/NanoPyx#150 · 4 comments · Opened Jan 14, 2026
Change modality parameter pixelsize_nm to take float Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

HenriquesLab/VLab4Mic#97 · Opened Dec 3, 2025
Modality pixelsize_nm must be divisible by psf_voxel_nm Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

HenriquesLab/VLab4Mic#96 · Opened Dec 3, 2025
Yolov2 notebook unable to run in Docker environment Open

bug

HenriquesLab/DL4MicEverywhere#59 · 1 comment · 1 assignee · Opened Oct 1, 2025
pix2pix_ZeroCostDL4Mic - Errors when launching from CLI Open

bug

HenriquesLab/DL4MicEverywhere#58 · 1 assignee · Opened Sep 26, 2025
VS Code Integration Tutorials Open

documentation enhancement good first issue help wanted

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

HenriquesLab/rxiv-maker#169 · 1 comment · Opened Sep 26, 2025
BioImage Model Zoo model doesn't export Open

bug

HenriquesLab/DL4MicEverywhere#57 · 1 assignee · Opened Aug 18, 2025
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
UNET-3D notebook - very slow training, performance bottleneck ? Open

bug

HenriquesLab/DL4MicEverywhere#55 · 1 assignee · Opened Oct 31, 2024
Splinedist failing to install dependencies Open

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

HenriquesLab/ZeroCostDL4Mic#328 · Opened Sep 24, 2024
StarDist_2D_ZeroCostDL4Mic.ipynb ImportError: cannot import name 'load_resource_description' from 'bioimageio.core' Open

bug

HenriquesLab/DL4MicEverywhere#54 · 1 assignee · Opened Sep 2, 2024
Error in U-Net_2D_Multilabel_ZeroCostDL4Mic.ipynb: IndexError: list index out of range Open

bug

HenriquesLab/DL4MicEverywhere#52 · 2 comments · 1 assignee · Opened Aug 26, 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
ValueError: could not broadcast input array from shape (256,256,3) into shape (256,256) Open

bug

HenriquesLab/DL4MicEverywhere#50 · 2 comments · 1 assignee · Opened Aug 23, 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
Install on HPC Cluster with Singularity Open

enhancement

HenriquesLab/DL4MicEverywhere#47 · 1 assignee · Opened Jun 19, 2024
Remote connection to servers with WIndows OS Open

enhancement

HenriquesLab/DL4MicEverywhere#44 · 13 comments · 2 assignees · Opened May 29, 2024
Single file executables Open

bug enhancement

HenriquesLab/DL4MicEverywhere#43 · 2 assignees · Opened May 20, 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
error in window 10 Open

help wanted question

HenriquesLab/DL4MicEverywhere#32 · 3 comments · 1 assignee · Opened Feb 6, 2024
Rootless installation and running Open

enhancement

HenriquesLab/DL4MicEverywhere#31 · 1 assignee · Opened Jan 24, 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
python versions constructor vs container dependencies Open

enhancement

HenriquesLab/DL4MicEverywhere#23 · 1 comment · 3 assignees · Opened Nov 17, 2023
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

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