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devel / comp.protocols.dicom / Data organization of Whole Slide DICOM image with multiple channels, resolutions, focus planes.

SubjectAuthor
* Data organization of Whole Slide DICOM image with multiple channels,Anil TA
`- Data organization of Whole Slide DICOM image with multipleDavid Clunie

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Data organization of Whole Slide DICOM image with multiple channels, resolutions, focus planes.

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Subject: Data organization of Whole Slide DICOM image with multiple channels,
resolutions, focus planes.
From: ta.anil007@gmail.com (Anil TA)
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 by: Anil TA - Mon, 4 Sep 2023 13:40 UTC

Hi,

Our scanner is generating images with multiple channels at multiple resolutions and at different depths.

We are able to convert an image which has multiple channels taken at different resolutions and successfully open them in SLIM DICOM viewer.

Our images are created and organized in the below way
For example, we have a image with 3 channels and acquired at 3 resolutions,

Channel 1 -- Resolution 1 -- Instance 1
Channel 1 -- Resolution 2 -- Instance 2
Channel 1 -- Resolution 3 -- Instance 3
Channel 2 -- Resolution 1 -- Instance 4
Channel 2 -- Resolution 2 -- Instance 5
Channel 2 -- Resolution 3 -- Instance 6
Channel 3 -- Resolution 1 -- Instance 7
Channel 3 -- Resolution 2 -- Instance 8
Channel 3 -- Resolution 3 -- Instance 9

Till here it is fine.

Now when the above image is acquired at different depths, then we fail to understand the data organization.

We tried, in the below way. But we get an error from SLIM viewer saying 'Uncaught Error: Multiple image instances for the same channel and focal plane have identical dimensions, but the instances are not part of a concatenation either. The image metadata is probably incorrect.'

Channel 1 -- Focus Level 1 - Resolution 1 -- Instance 1
Channel 1 -- Focus Level 1 - Resolution 2 -- Instance 2
Channel 1 -- Focus Level 1 - Resolution 3 -- Instance 3
Channel 1 -- Focus Level 2 - Resolution 1 -- Instance 4
Channel 1 -- Focus Level 2 - Resolution 2 -- Instance 5
Channel 1 -- Focus Level 2 - Resolution 3 -- Instance 6
Channel 1 -- Focus Level 3 - Resolution 1 -- Instance 7
Channel 1 -- Focus Level 3 - Resolution 2 -- Instance 8
Channel 1 -- Focus Level 3 - Resolution 3 -- Instance 9

Channel 2 -- Focus Level 1 - Resolution 1 -- Instance 10
Channel 2 -- Focus Level 1 - Resolution 2 -- Instance 11
Channel 2 -- Focus Level 1 - Resolution 3 -- Instance 12
Channel 2 -- Focus Level 2 - Resolution 1 -- Instance 13
Channel 2 -- Focus Level 2 - Resolution 2 -- Instance 14
Channel 2 -- Focus Level 2 - Resolution 3 -- Instance 15
Channel 2 -- Focus Level 3 - Resolution 1 -- Instance 16
Channel 2 -- Focus Level 3 - Resolution 2 -- Instance 17
Channel 2 -- Focus Level 3 - Resolution 3 -- Instance 18

Channel 3 -- Focus Level 1 - Resolution 1 -- Instance 19
Channel 3 -- Focus Level 1 - Resolution 2 -- Instance 20
Channel 3 -- Focus Level 1 - Resolution 3 -- Instance 21
Channel 3 -- Focus Level 2 - Resolution 1 -- Instance 22
Channel 3 -- Focus Level 2 - Resolution 2 -- Instance 23
Channel 3 -- Focus Level 2 - Resolution 3 -- Instance 24
Channel 3 -- Focus Level 3 - Resolution 1 -- Instance 25
Channel 3 -- Focus Level 3 - Resolution 2 -- Instance 26
Channel 3 -- Focus Level 3 - Resolution 3 -- Instance 27

Tags related to depth (like, Image Volume Depth, Z-Offset in Slide Co-Ordinate System, etc) are created correctly.

Any thing wrong in the above described organization ? Any clue would help us.

Regards,
Anil TA

Re: Data organization of Whole Slide DICOM image with multiple channels, resolutions, focus planes.

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Subject: Re: Data organization of Whole Slide DICOM image with multiple
channels, resolutions, focus planes.
From: dclunie@dclunie.com (David Clunie)
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 by: David Clunie - Tue, 5 Sep 2023 19:57 UTC

Hi Anil

I don't know if Slim supports more than one Z-depth (focal plane), whether they be in the same instance or separate instances - I suggest you raise an issue and supply some samples at the github site, which is now under the auspices of IDC: "http://github.com/ImagingDataCommons/idc-slim".

You might also want to check what BioFormats and OpenSlide (and thence apps like QuPath) do with DICOM images with more than one Z-depth:

https://github.com/ome/bioformats/pulls?q=is%3Apr+dicom
https://github.com/ome/bioformats/pulls?q=is%3Apr+z+depth

https://github.com/openslide/openslide/pull/431

They are looking for challenging samples to test with.

David

On Monday, September 4, 2023 at 9:40:33 AM UTC-4, Anil TA wrote:
> Hi,
>
> Our scanner is generating images with multiple channels at multiple resolutions and at different depths.
>
> We are able to convert an image which has multiple channels taken at different resolutions and successfully open them in SLIM DICOM viewer.
>
> Our images are created and organized in the below way
> For example, we have a image with 3 channels and acquired at 3 resolutions,
>
> Channel 1 -- Resolution 1 -- Instance 1
> Channel 1 -- Resolution 2 -- Instance 2
> Channel 1 -- Resolution 3 -- Instance 3
> Channel 2 -- Resolution 1 -- Instance 4
> Channel 2 -- Resolution 2 -- Instance 5
> Channel 2 -- Resolution 3 -- Instance 6
> Channel 3 -- Resolution 1 -- Instance 7
> Channel 3 -- Resolution 2 -- Instance 8
> Channel 3 -- Resolution 3 -- Instance 9
>
> Till here it is fine.
>
> Now when the above image is acquired at different depths, then we fail to understand the data organization.
>
> We tried, in the below way. But we get an error from SLIM viewer saying 'Uncaught Error: Multiple image instances for the same channel and focal plane have identical dimensions, but the instances are not part of a concatenation either. The image metadata is probably incorrect.'
>
> Channel 1 -- Focus Level 1 - Resolution 1 -- Instance 1
> Channel 1 -- Focus Level 1 - Resolution 2 -- Instance 2
> Channel 1 -- Focus Level 1 - Resolution 3 -- Instance 3
> Channel 1 -- Focus Level 2 - Resolution 1 -- Instance 4
> Channel 1 -- Focus Level 2 - Resolution 2 -- Instance 5
> Channel 1 -- Focus Level 2 - Resolution 3 -- Instance 6
> Channel 1 -- Focus Level 3 - Resolution 1 -- Instance 7
> Channel 1 -- Focus Level 3 - Resolution 2 -- Instance 8
> Channel 1 -- Focus Level 3 - Resolution 3 -- Instance 9
>
> Channel 2 -- Focus Level 1 - Resolution 1 -- Instance 10
> Channel 2 -- Focus Level 1 - Resolution 2 -- Instance 11
> Channel 2 -- Focus Level 1 - Resolution 3 -- Instance 12
> Channel 2 -- Focus Level 2 - Resolution 1 -- Instance 13
> Channel 2 -- Focus Level 2 - Resolution 2 -- Instance 14
> Channel 2 -- Focus Level 2 - Resolution 3 -- Instance 15
> Channel 2 -- Focus Level 3 - Resolution 1 -- Instance 16
> Channel 2 -- Focus Level 3 - Resolution 2 -- Instance 17
> Channel 2 -- Focus Level 3 - Resolution 3 -- Instance 18
>
> Channel 3 -- Focus Level 1 - Resolution 1 -- Instance 19
> Channel 3 -- Focus Level 1 - Resolution 2 -- Instance 20
> Channel 3 -- Focus Level 1 - Resolution 3 -- Instance 21
> Channel 3 -- Focus Level 2 - Resolution 1 -- Instance 22
> Channel 3 -- Focus Level 2 - Resolution 2 -- Instance 23
> Channel 3 -- Focus Level 2 - Resolution 3 -- Instance 24
> Channel 3 -- Focus Level 3 - Resolution 1 -- Instance 25
> Channel 3 -- Focus Level 3 - Resolution 2 -- Instance 26
> Channel 3 -- Focus Level 3 - Resolution 3 -- Instance 27
>
> Tags related to depth (like, Image Volume Depth, Z-Offset in Slide Co-Ordinate System, etc) are created correctly.
>
> Any thing wrong in the above described organization ? Any clue would help us.
>
> Regards,
> Anil TA

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