<div dir="ltr">Hi everyone,<div><br></div><div><div>One quick word of caution to Lewis and anyone else using the omeMeta.getPlane* methods.</div></div><div><br></div><div>> <span style="font-family:arial,sans-serif;font-size:13px">deltaT = double(omeMeta.getPlaneDeltaT(</span><span style="font-family:arial,sans-serif;font-size:13px">iSeries, iPlane));</span></div>
<div><br></div><div>The above call gets the DeltaT for Image #iSeries, Plane #iPlane. However, there is no explicit guarantee that that value corresponds to any particular (Z, C, T) coordinate triple. But you can check what the (Z, C, T) coordinates are for a given plane number using:<br>
</div>
<div><br></div><div> omeMeta.getPlaneTheZ(iSeries, iPlane);</div><div></div><div> omeMeta.getPlaneTheC(iSeries, iPlane));</div><div><div> omeMeta.getPlaneTheT(iSeries, iPlane);<br></div><div><br>
</div><div><div>> java.lang.IndexOutOfBoundsException: Index: 0, Size: 0</div></div><div><br></div><div>The IndexOutOfBoundsException happens if there is no Plane #iPlane in the metadata. You can determine that in advance using:</div>
<div><br></div><div> omeMeta.getPlaneCount(iSeries);</div><div><br></div></div><div>There is a complete example of how to extract planar timings at:</div><div><br></div><div> <a href="https://github.com/openmicroscopy/bioformats/blob/v4.4.8/components/bio-formats/utils/PrintTimestamps.java" target="_blank">https://github.com/openmicroscopy/bioformats/blob/v4.4.8/components/bio-formats/utils/PrintTimestamps.java</a><br>
</div><div><br></div><div>It is in Java but the calls from MATLAB are analogous.</div><div><br></div><div>Regards,</div><div>Curtis</div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Fri, Jun 7, 2013 at 9:29 AM, Melissa Linkert <span dir="ltr"><<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Hi Lewis,<br>
<br>
There is now a ticket on our issue tracking system to fix timestamp<br>
population for FV1000 .oib and .oif files:<br>
<br>
<a href="http://trac.openmicroscopy.org.uk/ome/ticket/11087" target="_blank">http://trac.openmicroscopy.org.uk/ome/ticket/11087</a><br>
<br>
If you would like to be automatically notified of changes to that<br>
ticket, please let us know and we will CC you.<br>
<br>
Regards,<br>
-Melissa<br>
<div><br>
On Fri, Jun 07, 2013 at 02:05:45PM +0000, Sebastien Besson wrote:<br>
> Dear Lewis,<br>
><br>
> thanks for uploading your raw data. We will take a look at it and check if timestamps are present in the file that could be read by Bio-Formats.<br>
><br>
> In general, copying the ome-users mailing list is recommended as it is likely other users will have similar questions/requests.<br>
><br>
> Best,<br>
> Sebastien<br>
><br>
> On 7 Jun 2013, at 13:43, Kraft, Lewis James wrote:<br>
><br>
> Thanks for your reply Sebastien. I really love the idea of this Bio-Formats project.<br>
><br>
</div>> Is there any hope of having the Plane – DeltaT metadata field added for the .oib files? It would be nice to have at least this feature working for the file formats from the big 4 microscopes. I uploaded some test data for the Bio-Formats project (ID: 7327<<a href="http://qa.openmicroscopy.org.uk/qa/feedback/7327/?token=3b2871d8289d90282cd70f95807e4c37" target="_blank">http://qa.openmicroscopy.org.uk/qa/feedback/7327/?token=3b2871d8289d90282cd70f95807e4c37</a>>).<br>
<div>><br>
> Unfortunately, I am a complete beginner when it comes to Java programming, and the details of the existing project, or I would offer my help adding the needed code. Perhaps there is an easier coding task that I might try to get my hands dirty with at first?<br>
><br>
> Also, please forgive me if I am flooding the ome-user mailing list with this message - I am not familiar with what to post, and what not to post.<br>
><br>
> Best,<br>
> Lewis<br>
><br>
> From: Sebastien Besson [mailto:<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>]<br>
> Sent: Friday, June 07, 2013 4:42 AM<br>
> To: Kraft, Lewis James<br>
</div>> Cc: OME-users <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><mailto:<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>><br>
<div><div>> Subject: Re: [ome-users] Nikon ND2 Time information<br>
><br>
> Hi Lewis,<br>
><br>
> first of all, I am forwarding this conversation to the ome-users mailing list.<br>
><br>
> Regarding your email, there is no PlaneDeltatT field for the .oib format as listed in <a href="http://www.openmicroscopy.org/site/support/bio-formats4/formats/olympus-fluoview-fv1000-metadata.html" target="_blank">http://www.openmicroscopy.org/site/support/bio-formats4/formats/olympus-fluoview-fv1000-metadata.html</a>.<br>
> Thus the error below is not informative but expected.<br>
><br>
> As shown in the metadata table above, you should be able to read the PixelsTimeIncrement instead, i.e. for the first image series:<br>
> timeIncrement = double(omeMeta.getPixelsTimeIncrement(0));<br>
><br>
> Hope this helps,<br>
> Sebastien<br>
><br>
> On 6 Jun 2013, at 22:51, Kraft, Lewis James wrote:<br>
><br>
><br>
> Dear Sebastien,<br>
><br>
> Today I tried to read an Olympus .oib file. I received the following error which I traced back to the following line of code:<br>
><br>
> time(index1)=double(omeMeta.getPlaneDeltaT(0,index1-1));<br>
><br>
> Java exception occurred:<br>
> java.lang.IndexOutOfBoundsException: Index: 0, Size: 0<br>
><br>
> at java.util.ArrayList.RangeCheck(Unknown Source)<br>
><br>
> at java.util.ArrayList.get(Unknown Source)<br>
><br>
> at ome.xml.model.Pixels.getPlane(Pixels.java:600)<br>
><br>
> at loci.formats.ome.OMEXMLMetadataImpl.getPlaneDeltaT(OMEXMLMetadataImpl.java:3631)<br>
><br>
> Do you have any ideas on what might have gone wrong?<br>
><br>
> Thanks much,<br>
> Lewis<br>
><br>
> From: Kraft, Lewis James<br>
> Sent: Friday, May 31, 2013 4:42 PM<br>
> To: 'Sebastien Besson'<br>
> Subject: RE: [ome-users] Nikon ND2 Time information<br>
><br>
> Dear Sebastien,<br>
><br>
> Ah Ha! You are exactly correct! Many thanks!<br>
><br>
> Cheers,<br>
> Lewis<br>
><br>
> From: Sebastien Besson [mailto:<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>]<br>
> Sent: Friday, May 31, 2013 4:41 PM<br>
> To: Kraft, Lewis James<br>
> Subject: Re: [ome-users] Nikon ND2 Time information<br>
><br>
> Hi Lewis,<br>
><br>
> This is because the series and the plane index are 0-based. So to retrieve the first plane of the first series, try<br>
> deltaT = double(omeMeta.getPlaneDeltaT(0,0))<br>
><br>
> Cheers,<br>
> Sebastien<br>
><br>
> On 31 May 2013, at 22:33, Kraft, Lewis James wrote:<br>
><br>
> Thanks for the replies! Forgive me, for I am a bit clueless about the Java part of the programming, I tried the following:<br>
><br>
> >> deltaT = double(omeMeta.getPlaneDeltaT(1,1))<br>
> Java exception occurred:<br>
> java.lang.IndexOutOfBoundsException: Index: 1, Size: 1<br>
><br>
> at java.util.ArrayList.RangeCheck(Unknown Source)<br>
><br>
> at java.util.ArrayList.get(Unknown Source)<br>
><br>
> at ome.xml.model.OME.getImage(OME.java:600)<br>
><br>
> at loci.formats.ome.OMEXMLMetadataImpl.getPlaneDeltaT(OMEXMLMetadataImpl.java:3631)<br>
><br>
> This resulted in the following error message from MATLAB. I am not sure if it is my lack of understanding of iSeries and iPlane in your example below?<br>
><br>
> Best,<br>
> Lewis Kraft<br>
><br>
> From: Sebastien Besson [mailto:<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>]<br>
> Sent: Friday, May 31, 2013 2:56 PM<br>
> To: Curtis Rueden<br>
</div></div>> Cc: Kraft, Lewis James; <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><mailto:<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>><br>
<div>> Subject: Re: [ome-users] Nikon ND2 Time information<br>
><br>
> Hi Lewis,<br>
><br>
> with your variable names, you should be able to use the following to extract the timestamp of the plane iPlane for the series iSeries:<br>
><br>
> deltaT = double(omeMeta.getPlaneDeltaT(iSeries, iPlane));<br>
><br>
> As Curtis said, if this call leads to an error, you can send a sample file.<br>
><br>
> Regards,<br>
> Sebastien<br>
><br>
> On 31 May 2013, at 20:42, Curtis Rueden wrote:<br>
><br>
> Hi Lewis,<br>
><br>
> > Where can I find this time information for each image plane in the<br>
> > .nd2 files?<br>
><br>
> It is best to extract the timestamp information from the OME metadata (specifically: OME > Image > Pixels > Plane > DeltaT), since it has been standardized to a format-agnostic structure. Then you won't have to worry about whether your file is .lsm or .nd2 or etc.<br>
><br>
> If the information is not present in the OME metadata, then it means Bio-Formats is not parsing and standardizing that information properly. In that case, if you send us a sample file (via <a href="http://qa.openmicroscopy.org.uk/qa/upload/" target="_blank">http://qa.openmicroscopy.org.uk/qa/upload/</a>), we can work on fixing the problem.<br>
><br>
> Regards,<br>
> Curtis<br>
><br>
</div><div>> On Fri, May 31, 2013 at 2:35 PM, Kraft, Lewis James <<a href="mailto:lewis.j.kraft@vanderbilt.edu" target="_blank">lewis.j.kraft@vanderbilt.edu</a><mailto:<a href="mailto:lewis.j.kraft@vanderbilt.edu" target="_blank">lewis.j.kraft@vanderbilt.edu</a>>> wrote:<br>
> Hello,<br>
><br>
><br>
> I am want to read the Nikon .nd2 image file using loci_tools.jar for MATLAB. I have successfully imported the image data using loci_tools.jar with the following MATLAB commands:<br>
><br>
> imgdata=bfopen(‘fullfilepath\*.nd2’); %command for opening images using BioFormats MATLAB scripts<br>
><br>
> img=imgdata{1,1}{1,1}; %First image in the timeseries<br>
><br>
> metadata=imgdata{1,2}; %Metadata in the .nd2 file<br>
><br>
> omeMeta = imgdata{1, 4}; %OME Metadata<br>
><br>
> The Image data, and the OME metadata look fine. However, the original metadata is missing the time information. For example, when opening Zeiss .lsm files, I see the time information in metadata as, “*TimeStamp*,*TimeStamp*,…”. Where can I find this time information for each image plane in the .nd2 files?<br>
><br>
><br>
> Thanks much,<br>
> Lewis Kraft<br>
><br>
><br>
><br>
> _______________________________________________<br>
> ome-users mailing list<br>
</div>> <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><mailto:<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>><br>
<div>> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
><br>
> _______________________________________________<br>
> ome-users mailing list<br>
</div>> <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><mailto:<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>><br>
<div><div>> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
><br>
> Dr Sébastien Besson<br>
> Open Microscopy Environment / Harvard Medical School<br>
> Wellcome Trust Centre for Gene Regulation and Expression,<br>
> College of Life Sciences, University of Dundee, Dow Street,<br>
> Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
><br>
><br>
> The University of Dundee is a registered Scottish Charity, No: SC015096<br>
><br>
> Dr Sébastien Besson<br>
> Open Microscopy Environment / Harvard Medical School<br>
> Wellcome Trust Centre for Gene Regulation and Expression,<br>
> College of Life Sciences, University of Dundee, Dow Street,<br>
> Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
><br>
><br>
> The University of Dundee is a registered Scottish Charity, No: SC015096<br>
><br>
> Dr Sébastien Besson<br>
> Open Microscopy Environment / Harvard Medical School<br>
> Wellcome Trust Centre for Gene Regulation and Expression,<br>
> College of Life Sciences, University of Dundee, Dow Street,<br>
> Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
><br>
><br>
> The University of Dundee is a registered Scottish Charity, No: SC015096<br>
><br>
> Dr Sébastien Besson<br>
> Open Microscopy Environment / Harvard Medical School<br>
> Wellcome Trust Centre for Gene Regulation and Expression,<br>
> College of Life Sciences, University of Dundee, Dow Street,<br>
> Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
><br>
><br>
> The University of Dundee is a registered Scottish Charity, No: SC015096<br>
<br>
> _______________________________________________<br>
> ome-users mailing list<br>
> <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br>
> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<br>
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</div></div></blockquote></div><br></div></div>