[ome-users] chunkmap bug with some nd2 files

[Vrtis, Kyle B.]

Thanks again. I have uploaded the sample file to the server.


180627 1e Cas9 GINS collapse lag lag.nd2


Best,


Kyle


________________________________
From: David Gault (Staff) <d.gault at dundee.ac.uk>
Sent: Friday, July 6, 2018 9:29 AM
To: OME User Support List; Vrtis, Kyle B.
Subject: Re: [ome-users] chunkmap bug with some nd2 files

Hi Kyle,

Thank you for sending in the report and taking the time to narrow down the problem. I have opened a Bio-Formats Trello card for the problem : https://trello.com/c/UtugDbmG/258-nd2-incorrect-sizet-when-chunkmap-enabled<https://urldefense.proofpoint.com/v2/url?u=https-3A__trello.com_c_UtugDbmG_258-2Dnd2-2Dincorrect-2Dsizet-2Dwhen-2Dchunkmap-2Denabled&d=DwMFAw&c=WO-RGvefibhHBZq3fL85hQ&r=3PbQOR8HqRwNi0bcVWWgMx0ICn__5BFLgc6JDycmRNs&m=RDNgA93L96Gx3fVF1z_D6crz2uFwdyXWcM4tghgAfLw&s=4NMkhANnU1hY1AUCZf6XcqknH9UNvyY5iNn2GI63OMU&e=>
It would be useful to have a sample file to reproduce the problem, since the files are > 2GB we will follow up with a private email to provide ftp access for sending the file.

With Thanks,
David Gault

On 5 Jul 2018, at 18:54, Vrtis, Kyle B. <Kyle_Vrtis at hms.harvard.edu<mailto:Kyle_Vrtis at hms.harvard.edu>> wrote:

Hello,

First of all, Bio-Formats is fantastic. Thanks!

I am having a reproducible issue with importing nd2 files. With some nd2 files (not sure why it is not all of my files) the number of images reported is wrong. For example I have one, large nd2 file that has a time lapse of 61 time points (512x512 px) across 60 series (3.85 GB file), but it imports with only 34 time points per series. The issue has been narrowed down to the "chunkmap" feature. When "chunkmap" is disabled, everything is correct (but importing is very slow). I have included a screenshot below of the same file loaded with "chunkmap" (left) and without it (right).

<pastedImage.png>


A second nd2 file recorded the same day with 70 series and 61 time points per FOV (4.5 GB file) does not have the issue. I would be happy to provide the files if it would help.

I am using the newest release of bio-formats and the issue is reproducible when I import with both Matlab and ImageJ. I am using a Mac OS 10.11.6. I believe the Java I am using is build 1.8.0_131-b11. Here is additional information:

width: 512 px
height: 512 px
number of channels: 2
Z slices: 1
timepoints: 61

Please let me know if there is any additional information you need.

Thanks,

Kyle

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