Fiji is not opening all series in CZI files

Dear Fiji community,

I am experiencing a problem since last week when opening CZI files.

I have created a macro that opens CZI files, including all the series that it contains. Now, unfortunately, my macro started to open only the first image even when that same file has more than one.

The line in question is: run("Bio-Formats Importer", "open=["+path+dir[filenr]+"] autoscale color_mode=Default open_all_series rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");

I tried to open these files manually and I still can’t get Fiji to open all the images. I also tried to launch the Bio-Formats Importer but got the same result.

Some updates were made but I have no idea if they have anything to do with this behavior.

Please help!

Best regards,
Clara Barreto

Is there any chance you are getting an error message in the log that you could share?

Unfortunately, I am not getting an error message…
The funny thing is that I can open all the series in CZI files on my computer at work. I have transferred that Fiji to my personal computer but the issue persists. I am out of ideas right now, so any suggestion is welcome.

Hi @ClaraBarreto, so you are using the same version of Bio-Formats on both computers (can find in the version in Help > About Plugins > Bio-Formats Plugins)?

When you open the files manually with the Bio-Formats Importer do you not see any series select dialog? Has the one image that opens performed autostitching with the remaining series?

Hi @ClaraBarreto,

can you provide a download for the CZI file?

And you might want to read this as well:

Dear Fiji community,

Many thanks for all the help!
I have managed to solve the issue by exploring Fiji further to comply with your suggestions.
The Windowless option was selected on the Bio-Formats configuration, even though I had not scripted it to be in my Macro, and the option to Open all series was not checked (this was scripted though and I do not know why it did not work since it has in the past).
I will describe what I did to avoid anyone getting stuck on the same issue.

By accessing the Plugins > Bio-Formats > Bio-Formats Plugins Configuration, I selected Formats and Zeiss CZI (which is the image format that I wish to work in this case) and unchecked the box Windowless (the others I have kept checked).
When I tried again to open the image by the “Drag & Drop” approach, or by launching the Bio-Formats in Plugins > Bio-Formats Importer, the Bio-Formats window popped up. I checked the Open all series option and clicked OK which opened all the series.
After I have done what I described the Macro works fine.

Hope someone, someday, finds this useful!

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