1.computational-cell-analytics / micro-sam
Segment Anything for Microscopy
+14 stars
from 730 · score 2.71
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Ranked by Attention Score: stars gained over the last 30 complete days
11 repositories by Attention Score · Oct 4, 2026 – Nov 2, 2026 (UTC)
2.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.
+3 stars
from 518 · score 1.39
3.Dana-Farber-AIOS / pathml
Tools for computational pathology
+3 stars
from 464 · score 1.39
4.brainglobe / brainglobe-atlasapi
A Python interface to access neuroanatomical atlases
+3 stars
from 187 · score 1.39
5.jungmannlab / picasso
A collection of tools for painting super-resolution images
+2 stars
from 148 · score 1.10
6.cytomining / pycytominer
Python package for image-based profiling
+2 stars
from 144 · score 1.10
7.brainglobe / cellfinder
Automated 3D cell detection in very large images
+1 stars
from 231 · score 0.69
8.seung-lab / cloud-volume
Read and write Neuroglancer datasets programmatically.
+1 stars
from 175 · score 0.69
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.
+1 stars
from 173 · score 0.69
10.brainglobe / brainreg
Automated 3D brain registration with support for multiple species and atlases.
+1 stars
from 150 · score 0.69
11.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