bioView3D - volume rendering for biologysts

bioView3D volume renderer is an open source and cross-platform application intended for biologists to visualize EM, Confocal, etc. 3D imagery. It runs on Windows, MacOS X and Linux. It's based on OpenGL and will run smooth on modern-fast hardware. bioVoxels supports popular 3D stack formats like Fluoview, Zeiss LSM, TIFF, BioRad PIC, etc.

bioView3D has all the necessary tools embedded - image interpolation and channel remapping. The model is contructed using meta-data so it's physically accurate. It's also possible to export screen into an image file.

Requirements: Video card supporting OpenGL 1.2 and lots of memory

Recommended platform: Intel Core2Duo, 2GB RAM, nVidia 7x series

Features

• Cross-platform with binaries for Windows, Mac, Linux
• Reads many bio image and video formats
• Reads meta-data from BioRad PIC, TIFF, Metamorph STK (uncompressed and LZW compressed), Fluoview TIFF, Carl Zeiss LSM 5, PSIA TIFF, Nanoscope II/III
• Has two modes of rendering: textures and voxels
• On-the-fly 3D visualization (mapping/enhancement) of multi-channel data
• Export of fly-over video to several popular formats: QuickTime, WMV, AVI, Flash, MPEG1/2/4, etc.
• Visualization of graphical annotations: XML GObjects

Quick Start

1. Select desired volume X/Y resolution (by using "Maximum size X/Y" combo box)
2. Load image (Using "Browse" button)
3. Choose channel mapping and transparency (by using "Channels" combo boxes and "Transparency" slider)
4. Render volume and interact with it (by pressing "Create volume" button)

Navigation

The navigation over the 3D sample is simple and can be done by only using mouse and it's buttons:

• Left button - Rotate the sample by X and Y axis
• Right button - Rotate the sample by X and Z axis
• Middle button - Pan the sample (move the volume relative to the sample's axis)
• Scroll wheel - Zoom the sample

Rendering

There are two rendering modes: the default is using 3D textures hardware support by the videocard, it renders smooth image very fast. The second mode is voxes based, in which boxes are rendered for each voxel, it works on every card but is much slower, though can be used for special tasks.

Movie export

There are two ways to export movie: the path based, in which the user can define visualization locations and number of frames and the movie will be interpolated accordingly. The second is the live mode in which frames are stored with user defined frequency. Movie export supports wide variety of formats and can generate Quicktime, Adobe Flash video, AVI, MPEG4 among others.

Register bioview3d protocol with Mozilla Firefox

Linux and Mac, as described in <http://kb.mozillazine.org/Register_protocol>

• Type about:config into the address bar and press Enter.
• Right-click -> New -> Boolean -> Name: network.protocol-handler.external.bioview3d -> Value -> true
• Right-click -> New -> String -> Name: network.protocol-handler.app.bioview3d -> Value -> /path/bin/bioView3D (Replacing /path/bin/bioView3D with the correct path)
• Ensure network.protocol-handler.expose-all is set to true.

Windows

The preferred way is to use the windows installer that does it automatically.
Or use the techinque described in: <http://kb.mozillazine.org/Register_protocol>