ClearVolume

KNIME Image Processing - Clear Volumne Integration

provided by MPI-CBG Dresden

About and Sceenshot

Interested in having a viewer for the TableCellView that can show 3D images or 4D images (3D + color channels) as beautiful volume renderings? If yes, this is your day!

ClearVolume is a volume renderer of this kind. Find further information here and/or here.

Fig. 1: ClearVolume is, after being installed, a tab in each TableCellView. This screenshot shows confocal microscopy data from adult fly brain. We thank Tzumin Lee's group at Janelia for being allowed to use their twin-spot MARCM (Yu et al., Nature Neuroscience, 2009) labeled neurons.

See ClearVolume in action here: https://www.youtube.com/watch?v=AjF-35vvwXY

How-To-Install

Currently, ClearVolume is only available with the NightlyBuild of KNIME Image Processing*. Therefore you have to conduct the following steps to install ClearVolume:

1. Download and install KNIME from http://www.knime.org/downloads/overview (without extensions, just KNIME)
2. Add Nighlty-Build Community Contributions Update-Site to KNIME: http://tech.knime.org/update/community-contributions/trunk (see http://tech.knime.org/wiki/install-knime-image-processing see step 2.2)
3. Install Clear Volume Integration

Please make sure that you have enough memory available. See: http://tech.knime.org/faq#q4_2

* this will change with the next 1.3.0 release of KNIME Image Processing.

FAQ

Do I need special hardware? Yes and no. Any computer with a graphics card capable of rendering OpenGL3.3 should be fine. If you encounter problems, please let us know... there are many setups out there and we can only test on the machines we have in our labs.

Do I want special hardware? Sure! With better graphics cards all will be smooth. If you have a Nvidia card we strongly suggest to install CUDA drivers. As soon as we find CUDA support we use it and this will significantly increase rendering speed.

 

Contact

Florian Jug
jug@mpi-cbg.de