Can sopa take as input COMET data ?

[reJELIN]

Dear Developers,

Could sopa take as input COMET data (https://lunaphore.com/products/comet/) ?

Best regards

[quentinblampey]

Hello @reJELIN,

What's the output of the COMET? Do you know where I can find any existing COMET datasets online?

Depending on the data format:

• if the data is standard (e.g., ome.tif files), then we can directly use an existing generic reader
• if the data is non-standard, we can quickly create a new COMET reader, it should be relatively straightforward, but I would need to download COMET data

[reJELIN]

You have an ome.tif (https://lunaphore.com/download-center-tma-downstream-analysis/)

But from what I understand it need to pass through HORIZON: https://lunaphore.com/products/horizon/

I was curious to see if sopa did better than their own coporate software but what's the point if they are doing a segmentation in the first place..

[quentinblampey]

Oh, okay, so it's multimodal, you also have transcripts. In that case, we'll need a dedicated reader.

The .ome.tif image is perfect, but how are the transcripts stored? We would need the x/y/z coordinates of the transcripts and their gene name.

Indeed, ideally we would like to avoid launching the HORIZON, but I'm afraid we would need the RNA-detection step, depending on what they have as a file format for the transcripts...