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Pyramids with small top levels #620

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s-n-i opened this issue Jul 29, 2022 · 3 comments · May be fixed by #633
Open

Pyramids with small top levels #620

s-n-i opened this issue Jul 29, 2022 · 3 comments · May be fixed by #633

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@s-n-i
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s-n-i commented Jul 29, 2022 •
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User story
I would like to be able to load a Zarr pyramid into Aviator, which has top levels in it that are smaller than the tile size on the lower levels. Doing so results in the image having a black box around it. The highest level of the pyramid is 1x1 pixel. I changed the canvas background-color in Avivator to white to make this clearly visible.

image

This black box is also present when I load a dataset without these top levels, but the black box is smaller in this case.

Preferred solution
Modify viv, such that it does not draw the black box.

Possible alternatives
An alternative solution would be to remove these top levels from the data. However, we would like to have them for a performance boost, when loading multiple pyramids at once.
@ilan-gold
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ilan-gold commented Jul 30, 2022 •
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Would it be possible to provide some data we could test on? I think most images have top levels smaller than the tile size, so I'm a bit confused - for example, this demo has top level 240x240 which is smaller than the tile size but renders fine. I think I'm not following what you are saying - the image you have looks like it has black pixels written into the image. You could actually fix this if you were using the layers directly by setting the transparentColor prop (although any other true black pixels in the real image would be transparent too).

@s-n-i
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s-n-i commented Aug 16, 2022

It took a bit of time for us to put together a live example because multiple people needed to be involved:

https://avivator.gehlenborglab.org/?image_url=https://viv-files.ci.aws.labshare.org/LuCa-7color_Scan_c(0-5)/

@ilan-gold
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Ok, I understand the issue now, sorry about the confusion. Zarr pads by default out to the chunk size i.e the tile size. @manzt I think we could implement something in the MultiscaleImageLayer to clip these low res tiles, no? Leave the loaders alone? We went through this a while ago so maybe I'm forgetting something.

@s-n-i s-n-i mentioned this issue Aug 24, 2022
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@ilan-gold ilan-gold linked a pull request Aug 25, 2022 that will close this issue
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feat(layers): Trim Top of Pyramids hms-dbmi/viv
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@ilan-gold @s-n-i