Formalizing and benchmarking open problems in single-cell genomics

Creating figures and animations for multi-channel images with a focus on microscopy.

A container registry for the scverse

Package management made easy

📈 Adaptive: parallel active learning of mathematical functions

Workshop repository for napari tutorial at DL@MBL 2024

A deep-learning based multi-modal data integration suite that aims to achieve synesis in a flexible manner

The repository provides code for running inference with the Meta Segment Anything Model 2 (SAM 2), links for downloading the trained model checkpoints, and example notebooks that show how to use th…

1 Line of code data quality profiling & exploratory data analysis for Pandas and Spark DataFrames.

Reimagine state management with CRDTs. Make your app collaborative effortlessly.

Python and R SOMA APIs using TileDB’s cloud-native format. Ideal for single-cell data at any scale.

Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports

a scalable data profiler

Quadra: Effortless and reproducible deep learning workflows with configuration files.

Image reading, metadata management, and image writing for Microscopy images in Python

Semi-continuous deployment of my PhD dissertation

Simple creation of data classes from dictionaries.

py.test fixture for benchmarking code

an SRT simulator for simulating multiple spatial variability in spatial resolved transcriptomics and generating unbiased simulated SRT data

A build-it-yourself AutoML Framework

Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.

Towards a general-purpose foundation model for computational pathology - Nature Medicine

upathlib

Techniques for deep learning with satellite & aerial imagery