1.computational-cell-analytics / micro-sam
Segment Anything for Microscopy
+40 stars
from 704 · score 3.71
Trending repositories
Ranked by Attention Score: stars gained over the last 90 complete days
19 repositories by Attention Score · Aug 5, 2026 – Nov 2, 2026 (UTC)
2.TIO-IKIM / CellViT
CellViT: Vision Transformers for Precise Cell Segmentation and Classification
+9 stars
from 390 · score 2.30
3.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.
+7 stars
from 514 · score 2.08
4.Dana-Farber-AIOS / pathml
Tools for computational pathology
+7 stars
from 460 · score 2.08
5.brainglobe / brainglobe-atlasapi
A Python interface to access neuroanatomical atlases
+7 stars
from 183 · score 2.08
6.jungmannlab / picasso
A collection of tools for painting super-resolution images
+6 stars
from 144 · score 1.95
7.sohmandal / classpose
A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources
+6 stars
from 33 · score 1.95
8.PytorchConnectomics / pytorch_connectomics
PyTorch Connectomics: segmentation toolbox for EM connectomics
+5 stars
from 197 · score 1.79
9.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.
+5 stars
from 169 · score 1.79
10.axondeepseg / axondeepseg
Axon/Myelin segmentation using Deep Learning
+3 stars
from 126 · score 1.39
11.brainglobe / cellfinder
Automated 3D cell detection in very large images
+2 stars
from 230 · score 1.10
12.brainglobe / brainreg
Automated 3D brain registration with support for multiple species and atlases.
+2 stars
from 149 · score 1.10
13.cytomining / pycytominer
Python package for image-based profiling
+2 stars
from 144 · score 1.10
14.pycroscopy / atomai
Deep and Machine Learning for Microscopy
+1 stars
from 229 · score 0.69
15.seung-lab / cloud-volume
Read and write Neuroglancer datasets programmatically.
+1 stars
from 175 · score 0.69
16.aelefebv / nellie
Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
+1 stars
from 97 · score 0.69
17.david-hoffman / pyotf
python functions for simulating optical transfer functions
+1 stars
from 85 · score 0.69
18.lens-biophotonics / ZetaStitcher
ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.
+1 stars
from 46 · score 0.69
19.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