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

James Wainwright jimboesq at gmail.com
Thu Feb 2 15:22:30 GMT 2017

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:


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

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