1.computational-cell-analytics / micro-sam
Segment Anything for Microscopy
+71 stars
from 673 · score 4.28
Trending repositories
Ranked by Attention Score: stars gained over the last 180 complete days
17 repositories by Attention Score · May 7, 2026 – Nov 2, 2026 (UTC)
2.TIO-IKIM / CellViT
CellViT: Vision Transformers for Precise Cell Segmentation and Classification
+24 stars
from 375 · score 3.22
3.Dana-Farber-AIOS / pathml
Tools for computational pathology
+16 stars
from 451 · score 2.83
4.sohmandal / classpose
A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources
+15 stars
from 24 · score 2.77
5.brainglobe / brainglobe-atlasapi
A Python interface to access neuroanatomical atlases
+12 stars
from 178 · score 2.56
6.PytorchConnectomics / pytorch_connectomics
PyTorch Connectomics: segmentation toolbox for EM connectomics
+11 stars
from 191 · score 2.48
7.jungmannlab / picasso
A collection of tools for painting super-resolution images
+11 stars
from 139 · score 2.48
8.zeiss-microscopy / OAD
Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.
+10 stars
from 164 · score 2.40
9.BMIRDS / deepslide
Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.
+9 stars
from 512 · score 2.30
10.cytomining / pycytominer
Python package for image-based profiling
+9 stars
from 137 · score 2.30
11.brainglobe / cellfinder
Automated 3D cell detection in very large images
+7 stars
from 225 · score 2.08
12.aelefebv / nellie
Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
+5 stars
from 93 · score 1.79
13.brainglobe / brainreg
Automated 3D brain registration with support for multiple species and atlases.
+4 stars
from 147 · score 1.61
14.axondeepseg / axondeepseg
Axon/Myelin segmentation using Deep Learning
+4 stars
from 125 · score 1.61
15.pycroscopy / atomai
Deep and Machine Learning for Microscopy
+3 stars
from 227 · score 1.39
16.david-hoffman / pyotf
python functions for simulating optical transfer functions
+3 stars
from 83 · score 1.39
17.davidbhr / CompactionAnalyzer
A python package to analyze the matrix fiber orientation and intensity around cells in fiber matrices (as a proxy for cellular forces).
+1 stars
from 11 · score 0.69