[ome-users] Bio-formats - opening IMS file problems

[David Gault (Staff)]

Hi James,

Thank you for submitting the sample QA files for this issue. I was able to test and reproduce the problems you described when importing through Fiji.
For further investigation into this I have added the details of these bugs to a card on the Bio-Formats 5.3 Trello board and a Trac ticket which you will be cc’d on http://trac.openmicroscopy.org/ome/ticket/13319#ticket.

With Thanks,
David Gault

On 2 Feb 2017, at 15:22, James Wainwright <jimboesq at gmail.com<mailto:jimboesq at gmail.com>> wrote:

Hi there,

I'm having some problems opening Imaris IMS files in FIJI.

I believe there is a partial workaround involving replacing the NetCDF jar with the latest one available here:

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp

This helps significantly, but there are still problems.

Having done some testing, I can confirm at least the following issues:

1) Time series data - there seems to be a frame limit around 7080 time points. Less than this will open, but more than this will not open with an error message. I have uploaded examples files using the QA system:

2016-12-14_08.43.34_Sample Prefix_WAINWRIGHT James_Protocol = 7075 frames (opens OK)
2016-12-14_09.26.04_Sample Prefix_WAINWRIGHT James_Protocol = 7081 frames (does not open)

2) 3D data - as you probably know, Imaris stores a number of different resolution volumes inside each IMS file. The problem seems to be that FIJI cannot open the largest of these. It offers only the smaller resolution. I have uploaded an example of this using the QA system:

2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol = 1024 x 1024 x 47 planes. FIJI seems to only offer the 512 and 256 pixel volumes.

Please let me know if there is anything else I can provide to try and help you resolve these issues? (No pun intended!).

Many thanks

James
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