Starred repositories
Large deformation diffeomorphic metric mapping (LDDMM) in PyTorch with KeOps library
Publication-quality OpenGL surface renderer with overlays — off-screen, Jupyter, and GUI support
A Library for presenting ome-zarr as ims files as a fuse mount
Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformations
Snakemake workflow for pulling cfmm dicom server data into bids
A minimalist production ready plugin system
An image processing package for removing streaks from SPIM images
GPU-based 3D non-rigid volumetric registration
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
An open-use web application created for easy access, collaboration, and sharing of datasets through rich metadata search, filter, sort, and direct viewing in common industry applications or in our …
A Python toolbox for aligning / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.
Build high-quality Laplace matrices on meshes and point clouds in Python. Implements [Sharp & Crane SGP 2020].
Fusing image tiles with dask array's map_blocks
An extremely fast Python package and project manager, written in Rust.
A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)
Command line tool to segment local and remote OME-Zarr data
Code for: Gaubert, M., Dell’Orco, A., Lange, C., Garnier-Crussard, A., Zimmermann, I., Dyrba, M., ... & Max, K. (2023). Performance evaluation of automated white matter hyperintensity segmentation …
BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)
A relabeling tool for tiled segmentation with Dask
A package to create simple 3D network visualizations on a brain.
Visualizer for large-scale and interactive ray-tracing of neurons
Dockerized web server for Neuroglancer and pre-computed images