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OMETIFF-TOOLS.md

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OME-TIFF Conversion and Viewing Tools

APEER OME-TIFF Library

  • Installation and release history
  • Uses tifffile to write the image
  • Uses bioformats module to generate OME-XML
  • OME-XML generated is bare-bones, must add TiffData elements for multi-page OME-TIFFs
  • Should also adjust filename, date, and channel elements
  • Previously used internal tool from Allen Cell Institute, but APEER is for public use and recieves feedback

FIJI

  • Installation guide
  • Does not require a server to run
  • Use bioformats plugin to validate/view OME-XML data (> Plugins > Bio-Formats > Bio-Formats Importer)
  • Good validation errors/warnings for incomplete OME-XML
  • Drag and drop or importer to view image (for large images, will sample image data for viewing)

OMERO

  • Installation guide
  • Requires a server to run, can request access to demo server
  • Must import data through the app, cannot import through website
  • Validation errors are not descriptive
  • Validation is possibly better than FIJI, given this is from the developers of OME-TIFF
  • Can view full resolution, colored image, can see composite of channels or toggle single channels on/off