help > Bioformat IO plugin build & run
Aug 7, 2012 05:08 PM | Bioformat IO plugin build & run I plan to release a new version later this month when I find
time... stay tuned. -Hanchuan ---------- Thank you for your reply. I indeed tried these things, including compiling the plugin separately with qmake. When I tried to make the whole package, I succeeded in getting a libimageIO_Bioformat_debug.dylib file. I tried dropping this into my working v3aad plugins directory, but this just caused v3aad to hang upon startup. I have java, as I am a heavy user of ImageJ, and I have loci_tools.jar in th same folder as the .app file. Can you send to me a precompiled plugi that I can drop into my plugins folder? Best regards, --aryeh On 7/31/12 11:26 PM, Peng PhD, Hanchuan wrote: I am a little busy right now but you can check
the readme in the plugin folder:
$ more how_to_build_and_run.txt To build this plugin, just following the normal Vaa3D plugin's qmake and make procedure. To run, you need to download the Loci bioformat jar file from: http://loci.wisc.edu/bio-formats/downloads and also ensure you have java on your machine. You need to copy the downloaded file "loci_tools.jar" to the Vaa3D executable folder (i.e. where you will find 'vaa3d', or 'vaa3d.exe', or 'vaa3d64.app', depending on your OS.) by Hanchuan Peng 2012-02-01 ________________________________________ From: [url=mailto:v3d-workgroup-bounces@listserv.janelia.org]v3d-workgroup-bounces@listserv.janelia.org[/url] [[url=mailto:v3d-workgroup-bounces@listserv.janelia.org]v3d-workgroup-bounces@listserv.janelia.org[/url]] on behalf of Aryeh Weiss [[url=mailto:aryeh@cc.huji.ac.il]aryeh@cc.huji.ac.il[/url]] Sent: Tuesday, July 31, 2012 4:03 PM To: [url=mailto:v3d-workgroup@listserv.janelia.org]v3d-workgroup@listserv.janelia.org[/url] Subject: [v3d-workgroup] starting with vaa3d I am just starting with this tool, and it looks great. However, I simply cannot get the bioformats plugin to work. It is not included in the distribution that I downloaded, and have no idea how to add it. I am using Mac OSX 10.6.8. I tried downloading and compiling the whole thing, as in the instructions: svn co https://svn.janelia.org/penglab/projects/vaa3d/trunk v3d_external svn co https://svn.janelia.org/penglab/projects/vaa3d_tools vaa3d_tools cd vaa3d_tools ln -s ../v3d_external/v3d_main v3d_main ln -s ../v3d_external/bin bin cd ../v3d_external ln -s ../vaa3d_tools/released_plugins released_plugins_more build.macx -B -m -j4 However, this ends with the following error: Find file [bin/plugins/data_IO/load_image_using_Bioformats/loci_tools.jar] The application cannot be opened because its executable is missing. So I add loci_tools.jar to bin/plugins/data_IO/load_image_using_Bioformats but this was erased at the next build, and then I get the same error. At this point I am stuck, because as nice as the tool is, I cannot use it if I will have to convert all of my OIB files. Any help would be greatly appreciated. --aryeh -- Aryeh Weiss Faculty of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384051 _______________________________________________ v3d-workgroup mailing list [url=mailto:v3d-workgroup@listserv.janelia.org]v3d-workgroup@listserv.janelia.org[/url] http://listserv.janelia.org/mailman/listinfo/v3d-workgroup --
Aryeh Weiss Faculty of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384051
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| Title | Author | Date |
| Bioformat IO plugin build & run | Hanchuan Peng | Aug 7, 2012 |
