ome-tiff

There are 0 repository under ome-tiff topic.

• cgohlke / tifffile

  Read and write TIFF files.

  format-readerimageimagejlife-sciences-imagenumpyome-tiffpythontiffwhole-slide-imagingzarr
  Language:Python 579

• hms-dbmi / viv

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

  gehlenborglabhubmapimagingome-tiffopenmicroscopyvivzarr
  Language:JavaScript 302

• ciccalab / SIMPLI

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

  cell-segmentationsingle-cell-analysisimaging-mass-cytometryimmunofluorescencehistological-imagesgatingtissue-analysistissue-classificationhistologybioimage-analysisbioimagingbioimage-toolsbioimage-informaticsmcdimclife-sciences-imageome-tiffimage-analysis-workflows
  Language:R 36

• tlnagy / OMETIFF.jl

  I/O operations for OME-TIFF files in Julia

  image-processingome-tiffjulia-languagejuliaome-filesmicromanagerimage-analysisimage-analysis-workflows
  Language:Julia 24

• BodenmillerGroup / imctools

  Tools to handle IMC data

  tiffmcdome-tiffimc-dataimc
  Language:Python 23

• Euro-BioImaging / BatchConvert

  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.

  bioimageconversionfile-formatimagenextflowomeome-zarrworkflowzarrome-zarr-converterome-tiff
  Language:Python 21
• HistoJS

  Mmasoud1 / HistoJS

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

  cell-cell-interactioncell-segmentationmibiscopemultiplexed-imagingmultiplexed-imaging-analysisome-tiffphenotypingproteomicsproteomics-data-analysissingle-cellwhole-slide-imagingdigital-slide-archiveimage-processingmultichannelspatial-biologyspatial-data-analysis
  Language:JavaScript 19

• nf-core / mcmicro

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

  nextflownf-corepipelineworkflowmicroscopymultiplexed-imagingspatialtmabioformatsome-tiffregistrationsegmentationstitchingimage-analysisimage-processingsingle-cell
  Language:Nextflow 12

• ome / ome-files-cpp

  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

  ome-tiffome-filescppreference-implementation
  Language:C++ 7

• ome / EMBO-Practical-Course-2023

  Advanced methods in bioimage analysis

  cloudngffomeome-ngffome-tiffome-zarrposixs3trainingzarr
  Language:Jupyter Notebook 6

• boonepeter / OME-Tiff-Csharp

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

  csharpome-tiffome-filestiff
  Language:C# 3

• SPerrott22 / Deepcell-to-QuPath

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

  cell-segmentationcodexfluorescence-microscopy-imagingmesmerome-tiffqupathdeepcellpaquo
  Language:Jupyter Notebook 3

• VasylVaskivskyi / image_registrator

  Feature based image registration for immunofluorescence images

  image-registrationimage-processingome-tiff
  Language:Python 3

• ome / ecdp2019-publication

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

  ome-tiffdigital-pathologywhole-slide-imagingproceedingssupplemental-materialsdockerbio-formatsomeroqupath
  Language:Python 2

• hzwirnmann / tcf_to_ometiff

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

  ome-tiff
  Language:Python 1

• hms-dbmi / viv-tile-benchmark

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

  ome-tiffgehlenborglabzarrviv
  Language:JavaScript

• tdiprima / medical-image-processing

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

  bio-formatsdcm4chedicomimage-analysismedical-image-processingocrome-tifftesseract
  Language:Java