<div dir="ltr">Hi Mirella,<div><br></div><div>Note also that Bio-Formats consists of Maven projects. In NetBeans, it should be as simple as File > Open Project... and select the toplevel Bio-Formats directory. Then you can open the Modules folder and double-click desired modules. I tested this just now with the "Bio-Formats command line tools" module (which has several example main methods) and was able to successfully build and run Bio-Formats code from within NetBeans.</div><div><br></div><div>For your own project, I strongly suggest using a modern build system such as Maven. Then you can simply add a dependency to e.g. ome:formats-gpl:5.1.10. There is really no need to manually manage your dependencies these days.</div><div><br></div><div>Regards,</div><div>Curtis</div><div class="gmail_extra"><br></div><div class="gmail_extra">P.S. If you extend the org.scijava:pom-scijava parent POM, the version of Bio-Formats and many other useful libraries is managed automatically for you. For details, see: <a href="http://imagej.net/Architecture" target="_blank">http://imagej.net/Architecture</a>, <a href="http://imagej.net/Maven">http://imagej.net/Maven</a></div><div class="gmail_extra"><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><span style="font-size:12.8px">--</span></div><div><span style="font-size:12.8px">Curtis Rueden</span><br></div><div><span style="font-size:12.8px">LOCI software architect - <a href="http://loci.wisc.edu/software" target="_blank">http://loci.wisc.edu/software</a></span></div><div>ImageJ2 lead, Fiji maintainer - <span style="font-size:12.8px"><a href="http://imagej.net/User:Rueden" target="_blank">http://imagej.net/User:Rueden</a></span></div><div>Did you know ImageJ has a forum? <a href="http://forum.imagej.net/" target="_blank">http://forum.imagej.net/</a></div><div><br></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Wed, Aug 3, 2016 at 4:00 AM, David Gault (Staff) <span dir="ltr"><<a href="mailto:d.gault@dundee.ac.uk" target="_blank">d.gault@dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div style="word-wrap:break-word">
Hi Mirella,
<div><br>
</div>
<div>In NetBeans the following steps should allow you to add the Bio-Formats libraries to your project:</div>
<div>- Right click on the your plugin project on the left hand panel and select Properties</div>
<div>- Under the Libraries category select 'Add Jar/Folder’</div>
<div>- Select the individual Bio-Formats jars or the folder containing them and select ‘Choose'</div>
<div>- You should now see the jars appearing in a Library folder in the Projects panel on the left</div>
<div><br>
</div>
<div>I hope that will be enough to get you up and running for your project.</div>
<div><br>
</div>
<div>With Thanks,</div>
<div>David Gault</div>
<div><br>
<div>
<blockquote type="cite"><span>
<div>On 2 Aug 2016, at 18:35, Mirella Koleva <<a href="mailto:mirella.koleva@dpag.ox.ac.uk" target="_blank">mirella.koleva@dpag.ox.ac.uk</a>> wrote:</div>
<br>
</span><div>
<div style="font-family:helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
Hi All,<u></u><u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
<u></u> <u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
I am using the NetBeans IDE to develop a plugin for ImageJ in the Java language. The plugin needs Bio-Formats to open the image to be analysed. I am new to using NetBeans and what I am having problems with is figuring out how to add the Bio-Formats Java libraries
to my NetBeans project.<u></u><u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
<u></u> <u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
I have searched very extensively on the internet for a solution and nothing seems to work.<u></u><u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
Amongst other things, I have tried:<u></u><u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
<u></u> <u></u></div>
</span><div style="margin:0cm 0cm 0.0001pt 36pt;font-size:11pt;font-family:calibri,sans-serif">
<span>1)<span style="font-style:normal;font-variant:normal;font-weight:normal;font-size:7pt;line-height:normal;font-family:"times new roman""> <span> </span></span></span>Downloading formats-gpl.jar
and putting it in the CLASSPATH and build path, as advised on the OME website<a href="http://www.openmicroscopy.org/site/support/bio-formats5.1/developers/java-library.html" style="color:purple;text-decoration:underline" target="_blank">http://www.openmicroscopy.org/site/support/bio-formats5.1/developers/java-library.html</a><u></u><u></u></div><span>
<div style="margin:0cm 0cm 0.0001pt 36pt;font-size:11pt;font-family:calibri,sans-serif">
<u></u> <u></u></div>
<div style="margin:0cm 0cm 0.0001pt 36pt;font-size:11pt;font-family:calibri,sans-serif">
<span>2)<span style="font-style:normal;font-variant:normal;font-weight:normal;font-size:7pt;line-height:normal;font-family:"times new roman""> <span> </span></span></span>Right-clicking on the
‘Dependencies’ folder of my NetBeans plugin project, selecting ‘Add Dependency…’, clicking on the ‘Dependency Management’ tab and selecting ‘ome : formats-gpl : [ jar ]’.<u></u><u></u></div>
<div style="margin:0cm 0cm 0.0001pt 36pt;font-size:11pt;font-family:calibri,sans-serif">
<u></u> <u></u></div>
<div style="margin:0cm 0cm 0.0001pt 36pt;font-size:11pt;font-family:calibri,sans-serif">
<span>3)<span style="font-style:normal;font-variant:normal;font-weight:normal;font-size:7pt;line-height:normal;font-family:"times new roman""> <span> </span></span></span>Adding a global library
in the Ant Library Manager by selecting Tools > Libraries, clicking on ‘New Library…’, then in both the ‘Classpath’ and ‘Sources’ tabs clicking on ‘Add JAR/Folder’ and choosing the right path to the .jar downloaded in 1).<u></u><u></u></div>
<div style="margin:0cm 0cm 0.0001pt 36pt;font-size:11pt;font-family:calibri,sans-serif">
<u></u> <u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
Regardless of this, NetBeans still doesn’t recognise the libraries I want to import: it underlines them in red and when I hover on the left-hand side over the warning icons, a pop-up bubble says ‘package does not exist’.<u></u><u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
<u></u> <u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
I am attaching here a snapshot of my screen.<u></u><u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
<u></u> <u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
I’d be very grateful for any tips regarding this issue!<u></u><u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
<u></u> <u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
With many thanks,<u></u><u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
<u></u> <u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:calibri,sans-serif">
Mirella<u></u><u></u></div>
</span></div>
<span><PrtScr_NetBeans.png></span><span style="font-family:helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline">_______________________________________________</span><br style="font-family:helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline">ome-devel
mailing list</span><br style="font-family:helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" style="color:purple;text-decoration:underline;font-family:helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br style="font-family:helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
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</blockquote>
</div>
<br>
</div>
<br>
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