ome-tiff

Read and write TIFF files.

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

Low-memory, zero-dependency image codecs and processing in pure TypeScript for Node.js, browsers, and serverless runtimes. Bounded decode/resize pipelines plus deep TIFF, scientific raster, GeoTIFF, OME-TIFF, and whole-slide support.

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.

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

I/O operations for OME-TIFF files in Julia

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

Unified API for streaming camera frames to either OME-TIFF or OME-Zarr format

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

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

Advanced methods in bioimage analysis

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

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

Feature based image registration for immunofluorescence images

OMIO is a Python library for reading, organizing, merging, visualizing, and exporting multidimensional microscopy image data under explicit OME-compliant axis and metadata semantics.

Fast whole-slide image optimizer. Repack/downsample/color-correct.

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

"Towards open and standardised imaging data" 28 May 2025