joshmoore
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NGFF
Convert an image stack to multiscale OME-NGFF Zarr
Algorithms for calculating a zarr checksum against local or cloud storage
Repo to document the ragged array idioms in oceanography
A napari plugin for use with xarray multiscale spatial images.
ImSwitch is a software solution in Python that aims at generalizing microscope control by providing a solution for flexible control of multiple microscope modalities.
A collection of Image Processing and Analysis (IPA) functions used at the Facility for Advanced Imaging and Microscopy (FAIM)
Fusing image tiles with dask array's map_blocks
Course materials for the practical on the Defragmentation Training School 2 - Porto, 8-12 May 2023
A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, in a parallelised manner.
Whole Slide image (WSI) conversion for brightfield histology images
A dataset for loading zarr files to be used in machine learning training pipelines
Java library for reading OME-Zarr data sets.
GIve easy, high-level access to ome-zarr fileset
Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)
Basic example of using OME-Zarr in a Nextflow pipeline
Get Your Brain Together Neuroimage Registration Workshops and Hackathons
Convert stacks of images to chunked datasets (and back)
A minimal Python package for reading OME-Zarr (meta)data
GUI Dialog to show structure of an ome.zarr dataset and to allow the user to cherry-pick image of interest, in Fiji.
Graph-based framework to manipulate and analyze cell lineages from cell tracking data
Simplifying image formats by consolidating file metadata into headers and footers