CZI: fluorescent channels not displaying
Opened this issue · 1 comments
This issue was first raised on image.sc thread: https://forum.image.sc/t/axioscan-7-fluorescent-channels-not-displaying-in-qupath/94615/15
A sample files showing the issue is available on Zenodo: https://zenodo.org/records/12533989
The sample file is a 9 channel image acquired with Axioscan 7 and contains a combination of fluorescent channels and a brightfield channel (TIE) for the same image
With Bio-Formats 7.3.0 we see a 9 channel image with 6 different resolution levels. The highest resolution level displays all 9 of the channels as expected. The remaining resolution levels however only show the 9th channel (TIE), the remaining channels are blank with 0 pixel values.
Series count = 1
Series #0 :
Resolutions = 6
sizeX[0] = 16728
sizeX[1] = 8364
sizeX[2] = 4182
sizeX[3] = 2091
sizeX[4] = 1045
sizeX[5] = 522
Image count = 9
RGB = false (1)
Interleaved = false
Indexed = true (false color, 16-bit LUT: 3 x 65536)
Width = 16728
Height = 13056
SizeZ = 1
SizeT = 1
SizeC = 9
With the CZI autostitch option turned off we get 63 series of 2040x2040, 9 channel images, each of which displays as expected.
This issue has been mentioned on Image.sc Forum. There might be relevant details there:
https://forum.image.sc/t/axioscan-7-fluorescent-channels-not-displaying-in-qupath/94615/17