Short Description

Use this plugin to quickly format volumetric data to display online with FPBioimage.
A new online tool for visualization of volumetric data: http://www.nature.com/nphoton/journal/v11/n2/full/nphoton.2016.273.html

Documentation

fpbioimagehelper is a plugin to make creation of a webpage for FPBioimage very straightforward. 

Open your 3D data in Icy, set the colormap of your choice, and press play on the plugin!

The plugin will generate a webpage and a directory of PNG image stacks, ready for rendering online with FPBioimage. Either save directly to a web server, or save to a location on your computer and upload to your web server at a later time. 

Note that to view your webpage offline, open Google Chrome with the flag '--allow-file-access-from-files'. More details on that here. 

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Changelog

  • Version 0.4.0.4 • Released on: 2018-08-01 18:13:40
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    Description:

    Updated template webpage to use https, which is now required by FPBioimage

  • Version 0.4.0.3 • Released on: 2018-02-28 14:18:52
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    Description:

    Latest version required for new Div name

  • Version 0.4.0.0 • Released on: 2018-02-22 00:58:58
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    Description:

    Updated FPBioimage Helper to work with the latest version of FPBioimage, bringing new rendering capabilities and a faster interface.

  • Version 0.3.9.16b • Released on: 2018-02-22 00:22:46
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    Description:

    Added some extra debugging log calls to try to find out what class loader works for loading jets3t library

  • Version 0.3.9.15 • Released on: 2018-02-22 00:07:20
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    Description:

    Uploaded the wrong file at 0.3.9.14b

  • Version 0.3.9.14b • Released on: 2018-02-22 00:04:31
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    Description:

    Switch class loader just before jets3t call; then switch back after

  • Version 0.3.9.13b • Released on: 2018-02-21 16:37:50
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    Description:

    See previous changelogs...

  • Version 0.3.9.12 • Released on: 2018-02-21 15:57:27
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    Description:

    Jar copied to somewhere I think it will be loaded from!

  • Version 0.3.9.11b • Released on: 2018-02-21 15:52:58
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    Description:

    Jets3t jar is added to the plugins folder if it doesnt exist already.

  • Version 0.3.9.10b • Released on: 2018-02-21 15:09:17
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    Description:

    All libraries now in fpblibraries, including jets3t...

  • Version 0.3.9.9b • Released on: 2018-02-21 15:01:41
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    Description:

    Trying to force loading all jets3t classes now

  • Version 0.3.9.8b • Released on: 2018-02-21 13:11:25
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    Description:

    Jets3t in separate library

  • Version 0.3.9.7b • Released on: 2018-02-21 13:02:59
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    Description:

    Added jets3t to its own library.

  • Version 0.3.9.6b • Released on: 2018-02-21 12:47:28
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    Description:

    Added jets3t jar as a resource, which should get copied into the plugins folder and so will be added to the classloader after a restart of Icy...

  • Version 0.3.9.5b • Released on: 2018-02-21 01:40:13
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    Description:

    Bundlled jets4t in...

  • Version 0.3.9.4 • Released on: 2018-02-18 23:19:27
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    Description:

    Moved the external libraries to a Plugin Libraries plugin, which will be a dependency of this plugin.

  • Version 0.3.9.3b • Released on: 2018-02-18 21:54:16
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    Description:

    Another change to the classpath

  • Version 0.3.9.2b • Released on: 2018-02-18 21:07:55
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    Description:

    Still trying to get classpath right...

  • Version 0.3.9.1b • Released on: 2018-02-18 18:31:40
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    Description:

    Still trying to get external libraries to work when not in debug mode

  • Version 0.3.9.0b • Released on: 2018-02-18 17:50:52
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    Description:

    Updated to use FPBioimage version 4.
    Might be having problems calling external java libraries still...

  • Version 0.3.0.8b • Released on: 2018-01-18 21:24:18
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  • Version 0.3.0.7b • Released on: 2018-01-10 17:56:00
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  • Version 0.3.0.6b • Released on: 2017-12-22 11:54:48
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    Description:

    Added a tickbox to upload images directly to FPB Host, a hosting service provided for FPBioimage data.

  • Version 0.3.0.5 • Released on: 2017-10-18 12:14:25
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    Description:

    Nicer website rendering

  • Version 0.3.0.4 • Released on: 2017-10-16 12:57:13
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    Description:

    Better template webpage, integration with latest version of FPBioimage (3.0.4)

  • Version 0.3.0.2b • Released on: 2017-10-10 00:47:59
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  • Version 0.3.0.1b • Released on: 2017-10-08 23:04:22
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    Description:

    Changed alpha export settings, to be in line with FPBioimage 3.0.1

  • Version 0.3.0.0b • Released on: 2017-06-28 12:59:18
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    Description:

    FPBioimage is now loaded directly from the server, so no need for your own installation - just upload the html file and image stack folder to anywhere on the web!
    Stacks are now saved as atlases, which reduces file sizes by about 30-40%.

  • Version 0.1.0.5 • Released on: 2017-05-22 10:29:09
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    Description:

    More bug fixes to copying template website.

  • Version 0.1.0.4b • Released on: 2017-05-22 10:04:39
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    Description:

    Some bug fixes on the template webpage.

  • Version 0.1.0.3b • Released on: 2017-05-18 17:12:41
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    Description:

    Updated the FPBioimage viewer and template webpage. Icy plugin may be buggy.

  • Version 0.1.0.2 • Released on: 2017-04-18 17:16:04
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    Description:

    Added clarity in section titles.

  • Version 0.1.0.1 • Released on: 2017-04-05 13:27:14
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    Description:

    Tool now opens the webpage (if requested) upon completion.

  • Version 0.1.0.0 • Released on: 2017-03-31 14:40:06
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    Description:

    Path to iamges is now relative to webpage, not to FPBioimage folder.
    Also some bug fixes regarding z-scaling, checking image size, and pressing cancel on save dialogs.

    Ready to come out of beta, I think!

  • Version 0.0.1.5b • Released on: 2017-03-23 15:44:47
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    Description:

    Installing FPBioimage from plugin should now work.
    Website should also work quite well.
    This means the plugin is almost ready to come out of beta, after a little more bug checking.

  • Version 0.0.1.4b • Released on: 2017-03-21 15:25:54
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    Description:

    Should have fixed problems with type conversion.

  • Version 0.0.1.3b • Released on: 2017-03-21 15:07:29
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    Description:

    Hopefully should be able to read html file in now. FPBioimage installation will still not work yet.

  • Version 0.0.1.2b • Released on: 2017-03-21 14:59:15
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    Description:

    Hopefully should be able to read html file in now. FPBioimage installation will still not work yet.

  • Version 0.0.1.1b • Released on: 2017-03-21 14:52:19
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    Description:

    Hopefully should be able to read html file in now. FPBioimage installation will still not work yet.

  • Version 0.0.1.0b • Released on: 2017-03-21 14:35:10
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