You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
{{ message }}
This repository has been archived by the owner on Jun 2, 2020. It is now read-only.
In #1, I noted that we should prefer the last two dimensions of the tiled arrays to be [y,x] as this is most efficient for accessing individual channels.
However, after looking at some whole slide images, I've found that RGB and RGBA images are mostly commonly stored as [x, y, rgba]. This means that for a 2 x 2 image, the data are stored interleaved like:
This makes sense because generally we will view rgba for a particular [x,y] slice together. napari guesses whether an array is RGB by looking at the shape of the array. If the last dimension is 3 or 4, it guesses RGB/RGBA, otherwise the last two dimensions are decided to be [y,x].
We should tile the last two dimensions preferably, but for RGB/RGBA images we should leave this last dimension as channels since this is most natural for WSI. We can use a rgb attribute in the base array to tell create_pyramid.py which dims to downsample and tile.
The text was updated successfully, but these errors were encountered:
Sign up for freeto subscribe to this conversation on GitHub.
Already have an account?
Sign in.
In #1, I noted that we should prefer the last two dimensions of the tiled arrays to be
[y,x]
as this is most efficient for accessing individual channels.However, after looking at some whole slide images, I've found that RGB and RGBA images are mostly commonly stored as
[x, y, rgba]
. This means that for a 2 x 2 image, the data are stored interleaved like:rather than
This makes sense because generally we will view rgba for a particular [x,y] slice together.
napari
guesses whether an array is RGB by looking at the shape of the array. If the last dimension is 3 or 4, it guesses RGB/RGBA, otherwise the last two dimensions are decided to be[y,x]
.We should tile the last two dimensions preferably, but for RGB/RGBA images we should leave this last dimension as channels since this is most natural for WSI. We can use a
rgb
attribute in the base array to tellcreate_pyramid.py
which dims to downsample and tile.The text was updated successfully, but these errors were encountered: