Slideseq cell coordinate unit
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13 months ago
morovatunc ▴ 560

Hello folks,

I am looking for information regarding the unit of the puck coordinates in slideseq data.

In the last section of the Puck Sequencing part in the 2019 science paper (doi: 10.1126/science.aaw1219), I see the following line.

The final stitched images were 6030 pixels by 6030 pixels.

My concern is I have been trying to combine multiple datasets. I see some even have negative X, Y coordinate which suggest that is centered.

Questions:

1) What is the unit of the X, Y coordinate (Pixels or microns?)

2) What is a good way to combine multiple datasets without worrying about the coordinate scale differences. (For instance, In Visium data, scale.json file contains the pixels covered each spot that allows swapping all of the coordinate values to microns.)

Its been so long since I asked a new question. I am once again asking for your wisdom.

Best, T.

Slideseq • 525 views
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Also asked here to the dev team of the raw-data processing tool. https://github.com/MacoskoLab/slideseq-tools/issues/51

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Entering edit mode

Alright so quoted line from the publication says the x,y coordinates of a puck is 0-->6030 pixels. I went through 2-3 datasets and found them all within the intervals. Not the best solution but I am ending my search here.

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