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Support ImSpector FLIM TIFF files #105

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cgohlke opened this issue Aug 26, 2024 · 2 comments · Fixed by #161
Open

Support ImSpector FLIM TIFF files #105

cgohlke opened this issue Aug 26, 2024 · 2 comments · Fixed by #161
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cgohlke commented Aug 26, 2024 •
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The FLUTE dataset currently used in the introductory tutorial consists of TCSPC FLIM data stored in OME-TIFF files with custom metadata, written by ImSpector Pro software.

While the files are valid OME-TIFF, the TCSPC histogram is misleadingly stored in the Z dimension (not in a H dimension), and the PhysicalSizeZ attribute apparently contains the TCSPC bin size in ns. The fundamental frequency in MHz can be calculated as 1000 / (SizeZ * PhysicalSizeZ).

No specification for this storage scheme and the custom metadata seems to be available.

Imspector also writes files in the MSR and OBF formats. Bio-Formats has a reader for MSR and OBF.

Here are the relevant parts from the OME-XML embedded in the Embryo.tif file:

...
<Image ID="Image:7B60FD74-9A87-465E-8A30-8B75D0C3C803" Name="t31_2h30DC-TCSPC_C0.ome.tif" DefaultPixels="Pixels:7B60FD74-9A87-465E-8A30-8B75D0C3C803">
<CreationDate>2021-11-05T12:30:27</CreationDate>
<Description>not_specified</Description>
<Pixels ID="Pixels:7B60FD74-9A87-465E-8A30-8B75D0C3C803" DimensionOrder="XYZTC" PixelType="uint16" BigEndian="false" SizeX="512" SizeY="512" SizeZ="56" SizeT="1" SizeC="1" PhysicalSizeX="1.179500" PhysicalSizeY="1.179500" PhysicalSizeZ="0.222909">
<TiffData>
<UUID FileName="t31_2h30DC-TCSPC_C0.ome.tif">urn:uuid:7B60FD74-9A87-465E-8A30-8B75D0C3C803</UUID>
</TiffData>
</Pixels>
<ca:CustomAttributes>
<Offset Offset_0="2.048004" Offset_1="2.048004" Offset_2="0.000000" Offset_3="0.000000"/>
<Length Length_0="603.904053" Length_1="603.904053" Length_2="12.482924" Length_3="1.000000"/>
<AxesLabels X="DC-TCSPC X" Y="DC-TCSPC Y" FirstAxis="DC-TCSPC T" SecondAxis="NONE" X-Unit="µm" Y-Unit="µm" FirstAxis-Unit="ns" SecondAxis-Unit=""/>
...
@cgohlke cgohlke self-assigned this Aug 26, 2024
@cgohlke cgohlke added the enhancement New feature or request label Aug 26, 2024
@cgohlke cgohlke mentioned this issue Sep 6, 2024
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cgohlke commented Dec 15, 2024

Requested documentation about the ImSpector FLIM TIFF format from Miltenyi Biotec.

@cgohlke cgohlke changed the title Support Imspector FLIM TIFF files? Support ImSpector FLIM TIFF files? Dec 15, 2024
@cgohlke cgohlke mentioned this issue Dec 15, 2024
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cgohlke commented Dec 17, 2024

Got some additional information about the ImSpector FLIM TIFF format from Miltenyi Biotec technical support (thank you).

The FirstAxis or SecondAxis attributes of the AxesLabels element in CustomAttributes can have the value 'lifetime' to identify the FLIM axis. The FLIM axis replaces either the regular T or Z axis, that is, either Z-stack or timelapse measurements are possible in FLIM mode.

This doesn't match the FLUTE sample files but should be added to the implementation.

@cgohlke cgohlke reopened this Dec 17, 2024
@cgohlke cgohlke mentioned this issue Dec 20, 2024
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@cgohlke cgohlke changed the title Support ImSpector FLIM TIFF files? Support ImSpector FLIM TIFF files Dec 20, 2024
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Add support for ImSpector FLIM TIFF files cgohlke/phasorpy
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