Read and write TIFF files.

Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.

SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

I/O operations for OME-TIFF files in Julia

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.

Tools to handle IMC data

HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇

pipeline that converts Deepcell generated instance segmentation masks of nuclei from an ome-tiff to Cell Objects with auto-generated cytoplasms in QuPath

OME Files is a C++ library for reading and writing data using the open and standard OME-TIFF file format using the OME data model

Advanced methods in bioimage analysis

C# helper class for serializing image metadata into Open Microscopy's OME-XML Tiff format.

Feature based image registration for immunofluorescence images

Supplementary information associated with Besson et al. (2019) ECDP 2019

Python tool to parse Tomocube TCF files to OME-TIFF format

"Towards open and standardised imaging data" 28 May 2025

Image Viewer for Digital Pathology at any scale. Part of the cytario platform.

A benchmark to compare data retrieval performance for OME-TIFF and Zarr using different tile sizes and HTTP protocol versions.

A Java Maven project demonstrating medical image processing techniques with Tesseract OCR, DCM4CHE DICOM tools, and Bio-Formats.