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2016_bray_natprot

Supporting data files, documentation, and updated tips for the Cell Painting protocol

2021_haghighi_submitted

High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations

airlocalize

Software for spot detection

applied-bioinformatics-iab2

An Introduction to Applied Bioinformatics, 2nd Edition

apt

Animal Part Tracker

ashlar

ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration

astropathpipeline

biapy

Open source Python library for building bioimage analysis pipelines

bioanalyze-docker-images

Docker Images for Jupyterhub + Bioinformatics

cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

cellpose

a generalist algorithm for cellular segmentation

cellpose_segmentation

Galaxy tool for for cell and nucleus segmentation using Cellpose

cellxgene-documentation

Documentation for the cellxgene product

clam

Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering

connected-components-3d

Connected components on discrete and continuous multilabel 3D & 2D images. Handles 26, 18, and 6 connected variants.

data-science-for-beginners

10 Weeks, 20 Lessons, Data Science for All!

decoupler-py

Python package to infer biological activities from omics data using a collection of methods.

denoiseg

Joint training of denoising and segmentation.

dnabarcodes

Simple generator of DNA barcodes for sequencing experiments

easi-fish

Tools and scripts for EASI-FISH image data analysis

elastix

Official elastix repository

fishscale

Spatial analysis of FISH data

fq-segmentation

Wrapper code for segmentation of cells and nuclei with Cellpose.

gutanalysistoolbox

Semi-automated analysis and characterisation of cells within the gut wall.

ijl-utilities-wrappers

Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)

infercnv

Inferring CNV from Single-Cell RNA-Seq

labkit-ui

Advanced Tool for Labeling And Segmentation

labs

Scripts for HarvardX courses: PH525x

lenstralab-smfish

mario-py

MARIO: single-cell proteomic data matching and integration using both shared and distinct features