Problem when opening PNG Image

Usage & Issues
#1

Using the last Fiji 64 bits windows version,I tried to open a PNG 8bits gray image, but it is opened as a 3 channels (R,G,B) image, with an inverted LUT.
You can test this using the following image: https://bioimagingcore.be/owncloud/index.php/s/mOqWDToMg3Uyq2f

This is how it is opened:

428Ɨ522 14.4 KB

Spot intensity value should be at 255 and background should be at 0, but Fiji invert the values and open it as a 3 artificial color channels image

#2

Good day Benjamin,

plain ImageJ-1 opens your image as 8bit gray-value with inverted LUT. The latter means that the spots have the correct value 255 but are only displayed in black.

Regards

Herbie

#3

Hi Herbie,

Thanks for testing, but this is not the case using Fiji, where should I report this bug ? I suspect a bug in Bioformat, which seems to be used instead of the javax.imageio.ImageIO class.

#4

The same is true for Fiji, as long as you have Use SCIFIO when opening files (BETA!) unchecked in Edit > Options > ImageJ2.

@bpavie Can you check if this setting is enabled by chance on your system? (It should be disabled by default in a fresh Fiji installationā€¦)

Donā€™t worry, this forum is the perfect place to report and discuss issues like this :slight_smile:

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#5

But the issue here - is it the inversion of the LUT and/or the fact it opens this 8-bit images as a 3-channel image?? Just curiousā€¦

#6

@bpavie How exactly are you opening your image? Via File > Import > Bio-Formats - the image is no longer invertedā€¦ but still renders as a 3-channel image.

#7

Youā€™re right indeed, the Use SCIFIO when opening files (BETA!) was checked (looks to be checked by default now).

@etadobson: If I drag and drop the image with the option Use SCIFIO when opening files (BETA!) checked, I got this issue.

Same using the following groovy code:
impSpot = IJ.openImage(Paths.get(dir.getAbsolutePath(), ā€˜spot-f.pngā€™).toString())

Using import bioformat give me the same result (with or without the option Use SCIFIO when opening files (BETA!) checked )

It could be a problem, because the same image could give 2 different ImagePlusā€¦

#8

The data are the same in fact. The difference is that ImageJ1.x has some special-casing for png and jpeg images that checks if all three channels of an RGB color image are the same, and displays a single 8-bit image in this case.

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#9

But the imagePlus is then different, with an inverted LUT and 3 channels in case it is openwith Bioformat shouldnā€™t it be more homogenized? In case you write a script (in my case), that give different result depending of if the user check this option.

#10

I created an issue on the Fiji github: https://github.com/fiji/fiji/issues/168
I also added a video that demonstrate the issue.

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