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



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