It is a well known bug of format itself that wasn't fixed (yet). You can
set the correct value manually: setVoxelSize(2.19, 2.19, 1.0,
"micron");
Dnia 06 sierpnia 2025 23:17 Cammer, Michael
<[email protected]> napisał(a):
I also tried downloading BioFormats 8.3 and replacing 8.1.1. This did
not solve the problem.
Then I tried updated using Help > Update, and this did not solve the
problem. It also didn't openthe menu we like to see about color mode,
splitting or not, etc.
I am also using a different computer than for the report I made earlier.
Help would be appreciated.
Thank you.
-----Original Message-----
From: Cammer, Michael <[email protected]>
Sent: Wednesday, August 6, 2025 4:25 PM
To: [email protected]
Subject: opening Zeiss CZI images with BioFormats 8.1.1 give inconsistent
spatial scales.
[EXTERNAL]
We have found that images saved with Zen Blue and opened with BioFormats do
not have correct spatial scales.
Images were generated with Zen 3.10.103.04000 and saved as CZI.
Using ImageJ 1.54q14 and the BioFormats version Zeiss gave us with a LSM800
upgrade, which is version 8.1.1 from 5 March 2025, images do not open with the
spatial scale. (We switched from our older preferred version of BioFormats
because it will not open new CZI format files.)
The original image has a 0.137 um pixel size.
We are opening pyramid #5, which is 1/16 full size, so we calculated that each
pixel should be 2.19 um/px.
When we were using the system earlier, BioFormats assigned no spatial scale.
The images were not calibrated.
To confirm the problem, I restarted Fiji and reopened the image. This time
the pixel spatial scale is reported as 0.1370000 micron, but this is incorrect.
The original 101384 x 101330 pixels image has this scale, but this 6336 x 6333
pixels image should have a scale claoser to 2.19 um.
Confused by the inconsistent behavior, I opened the file as pyramid level #4
which is 12673 x 12666 pixels. It also has the calibration set to 0.137 um.
Is this a known bug?
Thank you!
Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory NYU Langone
Health, 540 First Avenue, New York, NY 10016
Office: RB (formerly Skirball) 4-102 -- call if door is locked (phone near
elevators)
Office: 646-501-0567 Cell (voice only, not text): 914-309-3270
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