bioformats

Here are 10 public repositories matching this topic...

nf-core / mcmicro

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

workflow pipeline nextflow image-processing spatial stitching registration segmentation image-analysis single-cell microscopy ome-tiff nf-core tma bioformats multiplexed-imaging

Updated Sep 11, 2026
Nextflow

andreped / vsi2tif

Star

Simple tool for converting WSIs from cellSens VSI to pyramidal TIFF

fast converter tiff generic openslide olympus vips vsi tif wsi pyramidal bioformats pyvips cellsens pyfast cucim bftools

Updated Jun 12, 2026
Jupyter Notebook

imaging-formats / bffile

Star

Modern Bio-Formats wrapper with clean lazy Python API

ome file-formats bioformats

Updated Jun 25, 2026
Python

Ebola-Chan-bot / Image5D

Star

5D图像读写库，全网最快第三方OIR读入器

image tiff olympus ome 5d bioformats oir

Updated Feb 12, 2026
C++

yfukai / pycziutils

Star

A tiny utility module to parse Zeiss CZI files in Python through python-bioformats.

python zeiss-czi-files bioformats

Updated Dec 9, 2021
Python

simaopseixas / alm-file-converter

Star

Python GUI microscopy file converter for ICS2, IMS, LIF, ND2, ZVI, TIFF, OME-TIFF and OME-Zarr bioimaging datasets.

Updated Jul 27, 2026
Python

Cytomine-ULiege / Cytomine-BioFormats

Star

A BioFormats wrapper for Cytomine PIMS

pims cytomine bioformats

Updated May 23, 2023
Groovy

bwmr / vsi2tif

Star

Take Olympus vsi stacks. Bleach-correct, write out ome-tiff. Save clicks.

microscopy olympus vsi fluorescence-data bioformats

Updated Jun 24, 2024
Python

Cytomine-ULiege / pims-plugin-format-bioformats

Star

plugin bioformats

Updated Jun 27, 2022
Python

tlambert03 / bioformats_jar

Sponsor

Star

(deprecated) meta-package to import bioformats_jar from scyjava

python ome bioformats

Updated May 27, 2022
Python

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