[ome-users] nd2 files opening with multiple series instead of time series

[Sebastien Besson (Staff)]

Dear Michael,

thanks for the additional troubleshooting. I also retested your sample file with the fix mentioned
by David in his previous email but the incorrect dimension detection persists. It looks like more
investigation and work will be required to address this problem.

I have record the bug alongside similar issues of the same kind in our Bio-Formats backlog [1]
where future progress on the resolution of this issue can be tracked.

Best regards,
Sebastien

[1] https://trello.com/c/LEjj3O3A/281-nd2-timepoints-are-split-into-series


On 14 Sep 2018, at 21:29, Cammer, Michael <Michael.Cammer at NYULANGONE.ORG<mailto:Michael.Cammer at NYULANGONE.ORG>> wrote:

We tried all four combinations of checkboxes of Nikon & Chunkmap and same results.
Cheers-
Michael

From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> On Behalf Of David Gault (Staff)
Sent: Thursday, September 13, 2018 5:53 AM
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] nd2 files opening with multiple series instead of time series

Hi Michael,

Thank you for sending in the report. This sounds like it may be related to a similar problem which we have recently put in place a fix for (https://github.com/openmicroscopy/bioformats/pull/3191<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_openmicroscopy_bioformats_pull_3191&d=DwMGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=f6LzGbXPPsRXRCRm9Of4so8BlLZqNxm-xuaHes0NUCU&s=cFL3TWfZD8iIg5bKQlBtw_-i96aMQJwS72SvonJ374Y&e=>). A short term workaround until this is released would be to disable the use of the native chunk map for ND2 files, you can see how to set the options in https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/options.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.openmicroscopy.org_bio-2Dformats_5.9.2_formats_options.html&d=DwMGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=f6LzGbXPPsRXRCRm9Of4so8BlLZqNxm-xuaHes0NUCU&s=3o3lW8c2BlwCxe4nv96Q0GZMYbVFy5BtvsR9FeoyvWs&e=>.

If you are still seeing the issue with the chunk map disabled then this is a separate issue, in which case uploading a sample file to https://www.openmicroscopy.org/qa2/qa/upload/<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.openmicroscopy.org_qa2_qa_upload_&d=DwMGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=f6LzGbXPPsRXRCRm9Of4so8BlLZqNxm-xuaHes0NUCU&s=iQ_EfJa4bZFwsS_g7hkKvEbyxbvtHJo-vHXOvsDHpcI&e=> would be great.

With Thanks,
David Gault

On 12 Sep 2018, at 22:52, Cammer, Michael <Michael.Cammer at NYULANGONE.ORG<mailto:Michael.Cammer at NYULANGONE.ORG>> wrote:

Last week we used a Nikon W1 spinning disk system.  2 channel Z series were taken at multiple positions through time.  Each XY location is a separate ND2 file.

When we open them with BioFormats 5.9.2 with jave 1.8, we are prompted for Series whereas they should be a single file of timepoints.  It’s easy to combine them with the macro below, but would be great to have them open as a single time series.  Happy to upload an example file if you would like.

Also, the title is doubled.

Thank you!


Best regards,
Michael Cammer

The macro to fix the problem afterwards:

    t = getTitle;
    run("Concatenate...", "all_open title=[nmg smc_xy1] open");
    run("Stack to Hyperstack...", "order=xyczt(default) channels=2 slices=31 frames=37 display=Composite");
    rename(t);
    // manually edit title on save

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