CZI: fluorescent channels not displaying

[dgault]

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.

[imagesc-bot]

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