Basic support for OME-TIFF 2D (single & multiple channels)

[rmaree]

Support préliminaire du OME-TIFF serait un plus indéniable pour microscopie autre que digital pathology. Infos format: https://www.openmicroscopy.org/site/support/ome-model/ome-tiff/

On pourrait dans un 1er temps se contenter de la 2D+c en testant sur deux exemples artificiels ici (à inclure dans test set?): https://www.openmicroscopy.org/site/support/ome-model/ome-tiff/data.html 2D (single image) 2D (3 channels) Via l'utilisation des ImageGroup/ImageSequence du data model. Le reste (time points,focal planes) pourra se faire de manière similiaire plus tard.

tiffinfo de "single-channel.ome.tif ":

TIFF Directory at offset 0x8 (8)
  Image Width: 439 Image Length: 167
  Resolution: 0, 0 pixels/cm
  Bits/Sample: 8
  Sample Format: signed integer
  Compression Scheme: None
  Photometric Interpretation: min-is-black
  Samples/Pixel: 1
  Rows/Strip: 1
  Planar Configuration: single image plane
  ImageDescription: <?xml version="1.0" encoding="UTF-8" standalone="no"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://ome-xml.org/wiki/OmeTiff. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2013-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:ce84aab7-bbf8-402c-b2a4-9d26ae0fe910" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2013-06 http://www.openmicroscopy.org/Schemas/OME/2013-06/ome.xsd"><Image ID="Image:0" Name="single-channel"><AcquisitionDate>2013-06-19T13:02:10</AcquisitionDate><Pixels DimensionOrder="XYZCT" ID="Pixels:0" SizeC="1" SizeT="1" SizeX="439" SizeY="167" SizeZ="1" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="single-channel.ome.tif">urn:uuid:ce84aab7-bbf8-402c-b2a4-9d26ae0fe910</UUID></TiffData></Pixels></Image></OME>
  Software: OME Bio-Formats

tiffinfo du multi-channel.ome.tif:

TIFF Directory at offset 0x8 (8)
  Image Width: 439 Image Length: 167
  Resolution: 0, 0 pixels/cm
  Bits/Sample: 8
  Sample Format: signed integer
  Compression Scheme: None
  Photometric Interpretation: min-is-black
  Samples/Pixel: 1
  Rows/Strip: 1
  Planar Configuration: single image plane
  ImageDescription: <?xml version="1.0" encoding="UTF-8" standalone="no"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://ome-xml.org/wiki/OmeTiff. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2013-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:45218302-aae3-42dd-8a5d-d2e3592f3632" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2013-06 http://www.openmicroscopy.org/Schemas/OME/2013-06/ome.xsd"><Image ID="Image:0" Name="multi-channel"><AcquisitionDate>2013-06-19T13:02:12</AcquisitionDate><Pixels DimensionOrder="XYZCT" ID="Pixels:0" SizeC="3" SizeT="1" SizeX="439" SizeY="167" SizeZ="1" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:2" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:45218302-aae3-42dd-8a5d-d2e3592f3632</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:45218302-aae3-42dd-8a5d-d2e3592f3632</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:45218302-aae3-42dd-8a5d-d2e3592f3632</UUID></TiffData></Pixels></Image></OME>
  Software: OME Bio-Formats
TIFF Directory at offset 0x12487 (74887)
  Image Width: 439 Image Length: 167
  Resolution: 0, 0 pixels/cm
  Bits/Sample: 8
  Sample Format: signed integer
  Compression Scheme: None
  Photometric Interpretation: min-is-black
  Samples/Pixel: 1
  Rows/Strip: 1
  Planar Configuration: single image plane
  ImageDescription:
  Software: OME Bio-Formats
TIFF Directory at offset 0x24906 (149766)
  Image Width: 439 Image Length: 167
  Resolution: 0, 0 pixels/cm
  Bits/Sample: 8
  Sample Format: signed integer
  Compression Scheme: None
  Photometric Interpretation: min-is-black
  Samples/Pixel: 1
  Rows/Strip: 1
  Planar Configuration: single image plane
  ImageDescription:
  Software: OME Bio-Formats