Opening an 80MB file will take 13 hours to load

Hello,

Just starting to use bio-formats to import *.czi files from a Zeiss microscope, and am new to this forum.

I’m trying to open “point time scan” images that are saved as 80000 frames of 1x500 pixel images, making a file about 80 MB. Eventually this needs to be stitched into a single 80000x500 pixel image for analysis.

If I only import the first 100 or so frames, things work fine, but it takes about a minute to load, one frame at a time, into a stack. This means that opening all 80000 frames will take about 13 hours! I’ve tried opening the full file, all 80000 frames, and left it running for a few hours at work, but it only got to several thousand frames loaded before I had to go leave. I’m running Windows 10 on a Dell T7500 workstation with 64 GB memory, so shouldn’t be any issues there.

Is there a faster way to open a stack like this?

Thanks!

Nathan

Hi @nluser, are you importing the file into FIJI? What all options are you using in Importer window? Are you able to share a sample file publicly which we can test?

Hello,

Thanks for the response. Yes, I’m importing into FIJI using Bio-Formats. The options in the importer window are all unckecked, except I set the range for the series I want to import (e.g. the first 100 frames, which takes <1 minute to import) and view the stacks in the data browser.

Since each frame in the time series stack is a single 1x500 image, a single frame opens up quickly, but getting all 80000 in there will take about 10 hours or more. I set it running last night, and the frames open one at a time, counting from 1 to 80000 very slowly…

I’ll see if I can post a sample file.

Nathan

Hi @nluser,

what ZEN version are you using and did you try to export the CZI directly from ZEN as an OME-TIFF?

Hello,

Good idea. Yes, I can open them in Zen (blue) and export as OME-TIFF files. But another problem arises: exporting all 80000 frames will still take several hours per file. I’ve tried exporting a few hundred frames as a single OME-TIFF file (takes several minutes to export) and then import into FIJI as a test. This works well, and the files open almost immediately. So I’m hopeful that instead of >13 hours per file I can now just work with 3 hours of saving/loading per file.

Still will take a very long time, but I’ll set up a batch process and let it run for a week… Oh well.

Thanks,
Nathan