.lif project files do not open to show all files in them

bio-formats

#1

Hello guys,

I’m having troubles with opening my .lif files in Fiji. I thought it might be a bioformats issue since it doesn’t show me the usual window as in the past.

I have several project files (all .lif) which in turn have several image files in them. However when I open them via Fiji using Bio-formats, I am only able to see the topmost file and not the others.
I’m using 1.51w Fiji, and 5.9.3 Bio-Formats on a macOS Mojave 10.14.2

Does anyone have an idea what could be going wrong here?

Best,
Navneet


#2

Hi Navneet,

If I understand correctly, when you open with Bio-Formats you see the Bio-Formats Importer options but you do not see the Series Options dialog to select the image and it opens the first in the series?

If you select the option ‘Display OME-XML metadata’ does the resulting XML only have a single Image element?

David Gault


#3

Hi David,

Actually, I don’t see the Bio-Formats Importer options either. I just get a Console window and the first file of the series.

I have attached a screen shot of what it looks like.

Best
Navneet


#4

Thanks Nevneet, that does seem unusual. Are you opening the file from the Bio-Formats plugin menu or from a script or macro?

To allow us to test and reproduce the issue, would you be able to upload a sample file showing this issues to https://www.openmicroscopy.org/qa2/qa/upload/?

David Gault


#5

Hi David,

I am opening it both using the Bio-Formats importer as well as the drag-drop functionality. I get the same results in both cases.
I have to add that this seems to be an issue on my system only as it opened as expected on a colleague’s computer (but Windows).

I have uploaded the file now and it has the ID: 27240.

Once again, thanks for your help with this issue.

Best,
Navneet


#6

Just to confirm that we received the uploaded file and I have been able to test it on macOS with the same FIJI and Bio-Formats versions. Unfortunately I was unable to reproduce the issue. Have you made any changes to the jars in your FIJI directory?