<div dir="ltr">Hi Allon,<div><br></div><div><div>> The code you sent works with a minor modification: it is necessary to</div><div>> convert the name into a string using char().</div></div><div><br></div><div style>Great, thanks for the information. Perhaps Sébastien (the primary bfopen maintainer) will integrate your changes.</div>
<div style><br></div><div style>One word of caution: it occurred to me after sending that code snippet that there may be a discrepancy between the Bio-Formats/Java 0-indexing and MATLAB's 1-based indices. Off the top of my head, I am not sure whether "getImageName(i)" should actually be "getImageName(i-1)" but would be worth double checking, just to be sure.</div>
<div style><br></div><div style>Regards,</div><div style>Curtis </div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jun 13, 2013 at 1:42 PM, Allon Klein <span dir="ltr"><<a href="mailto:Allon_Klein@hms.harvard.edu" target="_blank">Allon_Klein@hms.harvard.edu</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"><div style="word-wrap:break-word">Hi Curtis,<div><br></div>
<div>Many thanks for the quick response. The code you sent works with a minor modification: it is necessary to convert the name into a string using char().</div><div><br></div><div>The code below adds the sequence name to the label without deleting any of the other information that bfopen helpfully includes. I added it to bfopen right after:</div>
<div> % build an informative title for our figure<br> label = id;<br><br></div><div><span style="white-space:pre-wrap"> </span>% NEW CODE</div><div><span style="white-space:pre-wrap"> </span> % add series name, if available<br>
<span style="white-space:pre-wrap"> </span>sequenceName = char(r.getMetadataStore().getImageName(i));<br><span style="white-space:pre-wrap"> </span>if ~isempty(sequenceName)<br><span style="white-space:pre-wrap"> </span>label = [label '; ' sequenceName];<br>
<span style="white-space:pre-wrap"> </span>end<br><br></div><div>Thanks again,</div><div>Allon<div><div class="h5"><br><div><div><br></div><div>On 13 Jun 2013, at 13:24, Curtis Rueden wrote:</div><br><blockquote type="cite">
<div dir="ltr">Hi Allon,<div><br></div><div>I am CCing the ome-users list, which is the best place to ask Bio-Formats questions.</div><div><br></div><div><div>> I just started using your matlab functions with loci-tools.jar. Thanks</div>
<div>> for making a wonderful tool!</div><div><br></div><div>Glad to hear it is working for you.</div><div><br></div></div><div><div>> I noticed a problem, which I suspect has a quick fix. When loading</div>
<div>> multiple series from a .lif file with bfopen, the image "labels" do</div><div>> not include the original series title. Instead, the bfopen script</div><div>> creates a "meaningful" label that includes information such as "series</div>
<div>> 1/23", but not the actual series label.</div><div><br></div><div>Indeed, it happens here:</div><div><br></div><div><a href="https://github.com/openmicroscopy/bioformats/blob/v4.4.8/components/bio-formats/matlab/bfopen.m#L200" target="_blank">https://github.com/openmicroscopy/bioformats/blob/v4.4.8/components/bio-formats/matlab/bfopen.m#L200</a></div>
<div><br></div><div>> This is clearly a matlab-implementation specific issue, because the</div><div>> series names are correctly recognized in the imageJ importer.</div><div><br></div><div>Right.</div><div><br></div>
<div>> I wonder whether you can suggest a quick hack to add this information?</div><div>> I tried looking up a user guide for loci-tools.jar, to see what</div><div>> command might retrieve the series names. But I couldn't find any</div>
<div>> information.</div><div><br></div><div>Sure, the code would be something like:</div><div><br></div><div># override label with series name, if available</div><div>imageName = r.getMetadataStore().getImageName(i);</div>
<div>if imageName ~= ""</div><div> label = imageName;</div><div>end</div><div><br></div><div>But I have not tested this, so it may need minor tweaking.</div><div><br></div><div>Regards,</div><div>Curtis</div></div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jun 13, 2013 at 9:13 AM, <span dir="ltr"><<a href="mailto:allon_klein@hms.harvard.edu" target="_blank">allon_klein@hms.harvard.edu</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">Allon Klein sent a message using the contact form at <a href="http://loci.wisc.edu/contact" target="_blank">http://loci.wisc.edu/contact</a>.<br>
<br>
Hi,<br>
<br>
I just started using your matlab functions with loci-tools.jar. Thanks for making a wonderful tool!<br>
<br>
I noticed a problem, which I suspect has a quick fix. When loading multiple series from a .lif file with bfopen, the image "labels" do not include the original series title. Instead, the bfopen script creates a "meaningful" label that includes information such as "series 1/23", but not the actual series label.<br>
<br>
This is clearly a matlab-implementation specific issue, because the series names are correctly recognized in the imageJ importer.<br>
<br>
For me having the series names is critical, since each series refers to a different condition and the details are stored in the names.<br>
<br>
I wonder whether you can suggest a quick hack to add this information? I tried looking up a user guide for loci-tools.jar, to see what command might retrieve the series names. But I couldn't find any information.<br>
<br>
Thanks very much, in advance, for your help!<br>
<br>
Best wishes,<br>
Allon Klein<br>
Systems Biology<br>
Harvard Medical School<br>
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