vanvalenlab/cellSAM

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Codebase for "A Foundation Model for Cell Segmentation"

Stars: 218
Forks: 39
Open beginner issues: 1
Indexed issues: 43

Dominant language: Python
License: Apache-2.0
Last GitHub push: Jun 4, 2026
Latest indexed: Sep 21, 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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Unable ro login to deepcell login Open

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

vanvalenlab/cellSAM#135 · Opened Sep 15, 2026
Unable to access CellSAM v1.2 weights due to DeepCell account registration/login issue Open

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

vanvalenlab/cellSAM#134 · 1 comment · Opened Aug 16, 2026
Unable to receive activation/password reset email from users.deepcell.org Open

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

vanvalenlab/cellSAM#133 · 2 comments · Opened Jul 22, 2026
Deepcell Registration Issue Open

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

vanvalenlab/cellSAM#132 · Opened Jun 10, 2026
register via the DeepCell porta Open

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

vanvalenlab/cellSAM#127 · 1 comment · Opened May 5, 2026
Unable to access users.deepcell.org and online demo; request for official CellSAM model access for academic research Open

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

vanvalenlab/cellSAM#125 · 1 comment · Opened Apr 13, 2026
I can't log in to the website https://users.deepcell.org/login/ with my email, and I can't download the pretrained model Open

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

vanvalenlab/cellSAM#124 · Opened Apr 12, 2026
I have completed the registration successfully, but I did not receive the verification email. Open

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

vanvalenlab/cellSAM#123 · Opened Mar 26, 2026
Unable to receive verification email after successful registration with `.edu.cn` address, and login always says username/password do not match Open

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

vanvalenlab/cellSAM#122 · Opened Mar 15, 2026
Registration request pending for 40+ days Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

vanvalenlab/cellSAM#121 · Opened Mar 9, 2026
Expanded TissueNet is Undocumented Open

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

vanvalenlab/cellSAM#120 · Opened Mar 7, 2026
Can't use cellSam because there's no way to get DEEPCELL_ACCESS_TOKEN Open

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

vanvalenlab/cellSAM#118 · 8 comments · 1 reaction · Opened Mar 4, 2026
Pre-trained model weights Open

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

vanvalenlab/cellSAM#116 · 4 comments · Opened Jan 24, 2026
Online CellSAM demo fails on official sample image Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

vanvalenlab/cellSAM#115 · 3 comments · Opened Jan 20, 2026
Stitching Causes Chopped Off Cells Open

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

vanvalenlab/cellSAM#113 · Opened Jan 14, 2026
iou_threshold Not Documented Below Function Prototype Open

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

vanvalenlab/cellSAM#112 · Opened Jan 14, 2026
Download Training Data Output Directory and Archive Size Open

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

vanvalenlab/cellSAM#111 · Opened Jan 5, 2026
CellSAM Boundaries are Much Bigger than the Cells Open

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

vanvalenlab/cellSAM#104 · Opened Nov 13, 2025
2D labels contain nested instances (cell fully inside another) Open

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

vanvalenlab/cellSAM#103 · 2 comments · Opened Oct 16, 2025
Multi GPU support Open

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

vanvalenlab/cellSAM#102 · 1 comment · Opened Oct 15, 2025
Pre-trained model weights - official release, version 1.2 Open

Models and Datasets

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

vanvalenlab/cellSAM#90 · 28 comments · 2 reactions · Opened Sep 12, 2025
Deployment at cellsam.deepcell.org transition to new infrastructure Open

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

vanvalenlab/cellSAM#75 · 1 comment · Opened Jul 29, 2025
Is This Preprocessing Pipeline Suitable for H&E-Stained RGB Input? Open

bug documentation

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

vanvalenlab/cellSAM#74 · 9 comments · Opened Jul 21, 2025
Apply segmentation to H&E images Open

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

vanvalenlab/cellSAM#63 · 1 comment · Opened Apr 10, 2025
Exporting to ONNX possible? Open

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

vanvalenlab/cellSAM#62 · Opened Apr 2, 2025
Wholeslide segmentation performance issues Open

bug

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

vanvalenlab/cellSAM#52 · Opened Mar 17, 2025
Ensure output labels are sequential Open

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

vanvalenlab/cellSAM#42 · Opened Feb 21, 2025
Single channel uint8 input fails with `low_contrast_enhancement=True` Open

bug

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

vanvalenlab/cellSAM#33 · 1 comment · Opened Feb 13, 2025
`cellsam_pipeline` interface Open

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

vanvalenlab/cellSAM#31 · 1 reaction · Opened Feb 13, 2025
Numpy version issue Open

bug

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

vanvalenlab/cellSAM#25 · 1 comment · Opened Sep 25, 2024
Model fine-tuning script Open

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

vanvalenlab/cellSAM#24 · 6 reactions · Opened Sep 18, 2024
CellFinder training Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

vanvalenlab/cellSAM#23 · 2 reactions · Opened Sep 11, 2024
Color flag in label layer creation in widget initiation for napari plugin is deprecated Open

bug

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

vanvalenlab/cellSAM#22 · 2 reactions · Opened Jul 16, 2024
Error 'numpy.ndarray' object has no attribute 'unsqueeze' when passing bounding boxes into segment_cellular_image Open

bug

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

vanvalenlab/cellSAM#21 · 1 reaction · Opened Jul 15, 2024
Bounding box prediction using other backbones Open

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

vanvalenlab/cellSAM#20 · 1 comment · Opened Jun 19, 2024
How to convert ground truth cell masks into bounding boxes Open

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

vanvalenlab/cellSAM#19 · 1 comment · Opened Jun 6, 2024
Model training script of CellSAM Open

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

vanvalenlab/cellSAM#18 · 3 comments · Opened Apr 13, 2024
Discussion: mask dtype Open

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

vanvalenlab/cellSAM#16 · Opened Apr 9, 2024
`segment_cellular_images` should always return the same output type Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 62/100

vanvalenlab/cellSAM#13 · 1 reaction · Opened Apr 3, 2024
Package name Open

Maintenance

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

vanvalenlab/cellSAM#10 · Opened Mar 30, 2024
napari plugin? Open

enhancement

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

vanvalenlab/cellSAM#5 · 2 comments · 1 reaction · Opened Mar 29, 2024
Most pre-processing functions and process_and_segment_image expect 3 dimensions, but percentile_threshold seems to expect 4 Open

bug

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

vanvalenlab/cellSAM#3 · 1 reaction · Opened Mar 25, 2024
Add option to pass bounding boxes to process_and_segment_image Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

vanvalenlab/cellSAM#2 · 1 reaction · Opened Mar 25, 2024

vanvalenlab/cellSAM

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