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gustaveroussy / sopa

Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
https://gustaveroussy.github.io/sopa/
BSD 3-Clause "New" or "Revised" License
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Immunofluorescence Image Segmentation #78

Open suhridbuddha opened 3 weeks ago

suhridbuddha commented 3 weeks ago

I have 3-channel immunofluorescence (DAPI, Cy5_Quad and FITC_Quad) image. Through CLI i am getting this error:

IncompleteFilesException:
The files below seem to be incomplete. If you are sure that certain files are not incomplete, mark them as complete with

    snakemake --cleanup-metadata <filenames>

the original meta data looks like this:

<?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 [http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"](http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd%22) UUID="urn:uuid:b78fd59f-1875-11ef-a2cd-480fcf6249ec" Creator="tifffile.py 2024.4.24"><Image ID="Image:0" Name="Image0"><Pixels ID="Pixels:0" DimensionOrder="XYCZT" Type="uint8" SizeX="44032" SizeY="76288" SizeC="3" SizeZ="1" SizeT="1" PhysicalSizeX="0.325" PhysicalSizeXUnit="m" PhysicalSizeY="0.325" PhysicalSizeYUnit="m"><Channel ID="Channel:0:0" SamplesPerPixel="1" Name="DAPI_Quad"><LightPath/></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1" Name="FITC_Quad"><LightPath/></Channel><Channel ID="Channel:0:2" SamplesPerPixel="1" Name="Cy5_Quad"><LightPath/></Channel><TiffData IFD="0" PlaneCount="3"/></Pixels></Image><Image ID="Image:1" Name="label"><Pixels ID="Pixels:1" DimensionOrder="XYCZT" Type="uint8" SizeX="1721" SizeY="1421" SizeC="3" SizeZ="1" SizeT="1" Interleaved="true"><Channel ID="Channel:1:0" SamplesPerPixel="3"><LightPath/></Channel><TiffData IFD="3" PlaneCount="1"/></Pixels></Image></OME>

Any idea on how to analyze IF images in SOPA ?

quentinblampey commented 3 weeks ago

Hello! What file format is it? .ome.tif I suppose? And does it come from a specific machine?

According to your error, it seems you were using the Snakemake pipeline, not the CLI. Can you show me which command you used to get this error? And can you try different readers using the API (like this ome.tif reader)?