norsimon
Image and data analyst at Harvard Medical School. Background: Physics. Numerical simulations, optics, bacterial cloning, stochastic differential equations, etc
Harvard Medical SchoolBoston, MA, USA
norsimon's Stars
janelia-cellmap/dacapo
A framework for easy application of established machine learning techniques on large, multi-dimensional images.
jeanollion/bacmman
HMS-IAC/Bioimage-Analysis-on-O2
Documentation page
quantumjot/btrack
Bayesian multi-object tracking
weigertlab/napari-trackastra
napari plugin for trackastra
paulssonlab/TrenchRipper
Small library for analysis of mother machine data. Built to run on a SLURM cluster, but can be run locally.
google-deepmind/penzai
A JAX research toolkit for building, editing, and visualizing neural networks.
MouseLand/cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
funkelab/motile
Multi-Object Tracker using Integer Linear Equations
miura/reproducible_bioimage_analysis
abo-abo/org-download
Drag and drop images to Emacs org-mode
segment-anything-models-java/SAMJ-IJ
An ImageJ/Fiji plugin designed to effortlessly integrate Segment-Anything models (SAMs) without code.
rkarmaka/SAM-using-Python-for-Microscopy-Data
gustaveroussy/sopa
Technology-invariant pipeline for spatial omics analysis (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / ...) that scales to millions of cells
ccb-hms/computervision
Everything to get started with computer vision
weigertlab/spotiflow
Accurate and efficient spot detection for microscopy data
kharchenkolab/Baysor
Bayesian Segmentation of Spatial Transcriptomics Data
hallvaaw/awesome-biological-image-analysis
A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
fonsp/Pluto.jl
🎈 Simple reactive notebooks for Julia
rivetTDA/rivet
RIVET is a tool for Topological Data Analysis, in particular two-parameter persistent homology.
giotto-ai/giotto-tda
A high-performance topological machine learning toolbox in Python
smegason/Goo
Goo is a Blender library for modeling biological cells, tissues, and embryos
JuliaImages/JuliaCon23_ImageProcessingWorkshop
norsimon/norsimon.github.io
personal scientific website
DeepTrackAI/DeepTrack2
DeepTrack2
computational-cell-analytics/micro-sam
Segment Anything for Microscopy
scverse/spatialdata
An open and interoperable data framework for spatial omics data
lutzroeder/minimal
Website and blog generator for Go, Node.js or Python
kwolbachia/Visualization_toolset
Imagej toolset to ease hyperstacks visualization and handling
facebookresearch/segment-anything
The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.