There are currently two issues with the downsampled image:
the images are saved at an unnecessarily high bit depth (probably 64 bit - ImageJ will load them as 32bit). The brightness values in those files appear unchanged from the original tiffs.
the orientation does not match the orientation of the atlas, instead it is saved as an x/y transposed version of the original image
There are currently two issues with the downsampled image:
the images are saved at an unnecessarily high bit depth (probably 64 bit - ImageJ will load them as 32bit). The brightness values in those files appear unchanged from the original tiffs.
the orientation does not match the orientation of the atlas, instead it is saved as an x/y transposed version of the original image