Problem of Image Quality

When I’m trying to open some images (in tiff format) for count the cell on it, my images become “pixelated” (like the exemple below). But with an other software, theses images are clear. I don’t know what’s happen, and I really need help because I can’t count cell on the “Figi-Image J” images like that and I need theses results soon as possible…!

Normal Image :
Normal image

Image on Image J :
Image J image

Thanks for your help.

Hi Laura and welcome to the forum :slight_smile:

Can you share a sample file that behaves in the manner you describe? Either upload here on the forum or share via dropbox/google drive or similar.

Which version of Fiji/ImageJ and Java are you running? Click the Fiji taskbar to see the current versions. On which operating system? Mac/Windows/Linux?

Hi thanks ^^

Here it is :

Image J version : 2.0.0-rc-43\1.51r
Java 1.6.0_24
Operating system : Windows 10 version 1703 [64-bit]

Thanks again :slight_smile:

I can reproduce this issue on W10, IJ 2.0.0-rc-61/1.151r, java 1.8.0_66 64bit. The image looks normal when opened in windows photo viewer but pixelated/snowy in IJ, either by direct opening or through bioformats importer.

How was this image acquired? Is this direct from the microscope? Which software? It is a three channel XY image, correct (just one z-slice)?

The image acquired on microscope Zeiss, on direct, on Zen 2 (as software). I don’t know what you mean by 3 channels… But a take this image in Brightfield (so, one channel I think), but this miscroscope have the particularity to take images in “tiles”, so the photo you seen, is a reconstruction of a lot photo on x40. However, I do the same extraction and acquisition for this picture than other one (few month ago), an the old ones worked fine …
Yes just one on the Z axis.

The metadata says it is 3 channels… I’m not sure why or if it is important. But I don’t know what is wrong, your old files still work or they also give bad images now?

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Old files work perfectly …
For the 3 channels, it’s very strange … I will look on Zen what’s happen about that. But I’m sure, I did the same acquisition for old and new pictures… I don’t know…

Dear Laura,
have you tried to zoom a lot either in the image opened with ImageJ and with the Windows Preview?

I have just tried with a MacOS and Preview and it seems to me that the whole image is rendered better in the Preview but when you zoom the image looks more or less the same in Fiji and in the Preview software.

whole image Fiji on the right


as @Sverre pointed out this acquisition is in RGB and it’s big 79*155.75 inches (you can check it in the upper part of the ImageJ/fiji image) but I don’t if it’s important

hoping it could be someway useful to investigate this issue.

Emanuele Maritni


@emartini You’re right it seems to be the same picture when we zoom in !
So it’s likely an acquision issue… I will check on the miscrocope.
Thanks a lot for your help ^^

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Hey everybody!
I have the same problem (I work with ImageJ 1.52 or 1.53).
In my case I have to analyse the pictures without zooming because I have to measure seedlings.
The picture quality is worse in ImageJ because the pictures are very pixelated but this is not normally the case.

My pictures are scans in jpg format and I used ImageJ in the last year to analyse them. Never had this problem before.
I don’t know what changed, my system hasn’t been changed (no connection to the internet).
I would be very relieved if someone has a solution for this problem because with this kind of pixelation I cannot distinguish between the roots or where one root ends next to some other root.

Its the picture on the left in ImageJ:
ImageJ problem 1 2021|300x500

Found a solution: removing the antivirus security and the problem was gone :slight_smile:

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