Thank you for the information. Are you saying that when Zeiss Zen generates the pyramid data it fails to set the metadata scale divided by 2 each time?
Best- Michael ________________________________ From: Ja <[email protected]> Sent: Thursday, August 7, 2025 3:06 AM To: [email protected] <[email protected]> Subject: Potential_SPAM:Odp: Re: opening Zeiss CZI images with BioFormats 8.1.1 give inconsistent spatial scales. [EXTERNAL] 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 [email protected]<mailto:[email protected]> urldefense.com https://urldefense.com/v3/__http://nyulmc.org/micros__; !!MXfaZl3l!fAZAEV9XA6G_SYYqNbDJFFmYVJfsCbyBKy4Xz8F4TIgFO_3ucfJE153NvVekhOu3L2Oe0B6FxzUvRPYlqiq7RjJdzI_rN8I8M2i3M4g$ urldefense.com https://urldefense.com/v3/__http://microscopynotes.com/__; !!MXfaZl3l!fAZAEV9XA6G_SYYqNbDJFFmYVJfsCbyBKy4Xz8F4TIgFO_3ucfJE153NvVekhOu3L2Oe0B6FxzUvRPYlqiq7RjJdzI_rN8I8-3wE8gY$ Scheduling the time you want is far more reliable by phone call. Why not provide your phone number? ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= -- ImageJ mailing list: urldefense.com https://urldefense.com/v3/__http://imagej.nih.gov/ij/list.html__; !!MXfaZl3l!fAZAEV9XA6G_SYYqNbDJFFmYVJfsCbyBKy4Xz8F4TIgFO_3ucfJE153NvVekhOu3L2Oe0B6FxzUvRPYlqiq7RjJdzI_rN8I8FtfvWGw$ -- ImageJ mailing list: imagej.nih.gov https://urldefense.com/v3/__http://imagej.nih.gov/ij/list.html__;!!MXfaZl3l!dQ-_t1VJiWftQwmTvAx5KB-gWUeuIAhLJhq1XLf9vbE_KldbyyDOm6_IBsJeZnABNDx9iwca3lcimKZ_J5lERZA$ -- ImageJ mailing list: https://urldefense.com/v3/__http://imagej.nih.gov/ij/list.html__;!!MXfaZl3l!dQ-_t1VJiWftQwmTvAx5KB-gWUeuIAhLJhq1XLf9vbE_KldbyyDOm6_IBsJeZnABNDx9iwca3lcimKZ_J5lERZA$ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
