Introduction

This page explains how to use the Remote Annotation and Multichannel Boundary Observer in 3D (Rambo3D).
It can be used for any of the data for which we have build the cutout service, which includes Bock11 and Kasthuri11. As more datasets become available, we will update here.

Installation

At this point, for prebuilt binaries we only provide a win32 executeable (VolumeViewer.exe). But we have successfully compiled it on mac and linux boxes.
If you have any trouble, just email [email protected].

Before you run the executable, make sure the driver of your video card is up to date (the generic one coming with windows does not work).

The general usage of the executable is:

VolumeViewer.exe --img img.data --ano ano.data --dRes xRes yRes zRes

where img.data and ano.data are the volumes downloaded from the cut-out service, and xRes/yRes/zRes together specify the data resolution.

Notice that the volume here needs to be a flattened hdf5 cube. For convenience in the package we provide a python script for doing that. To run the script, you you will need to have Python installed along with NumPy and h5py (whose win7-64 installers are all included in the package as well).

For now, the easiest way to get through the whole plumbing process is to use the provided batch script (demo.bat):

Demo Script

:: Specify here the minimum coordinate of the bounding box

SET XSTART=5000
SET YSTART=8000
SET ZSTART=968

:: Specify here the size (#voxels) of the data

SET XRES=512
SET YRES=512
SET ZRES=64

:: Leave the rest untouched

SET /A XEND=%XSTART%+%XRES%
SET /A YEND=%YSTART%+%YRES%
SET /A ZEND=%ZSTART%+%ZRES%
SET ANNO=http://openconnecto.me/annotate/kanno/hdf5/1/%XSTART%,%XEND%/%YSTART%,%YEND%/%ZSTART%,%ZEND%/
SET IMGS=http://openconnecto.me/cutout/kasthuri11/hdf5/1/%XSTART%,%XEND%/%YSTART%,%YEND%/%ZSTART%,%ZEND%/
hdf5Flatten.py %ANNO% ano.data
hdf5Flatten.py %IMGS% img.data
VolumeViewer.exe --dRes %XRES% %YRES% %ZRES% --img img.data --ano ano.data

User Interface

Mouse

• Right mouse button: drawing the zoom-in box

• LEFT mouse button: translating the camera

• MIDDLE mouse button: rotating the camera

• WHEEL: moving camera backward/forward

• SHIFT + WHEEL: advancing the viewing plane (same as SHIFT+UP/DOWN)

• SHIFT + RIGHT: rotating the viewing plane around the pivot

• SFHIT + LEFT: translating the pivot

KEYBOARD

• UP : moving the camera forward

• DOWN: moving the camera backward

• SHIFT+UP : moving the viewing plane forward

• SHIFT+DOWN: moving the viewing plane backward

• R: resetting the viewing plane

• Q,W: rotation around Y axis

• A,Z: rotation around X axis

• S,X: rotation around Z axis

• 3: setting the viewing plane to X-Y plane

• SHIFT+3: resetting the camera to look at X-Y plane from top (Simiarly for 1 and 2)

• O: toggle orthographics/perspective projection

• Esc: exit the viewer

Notes

If there is any problem, let me know at: [email protected]

--Ming

PS1. The plumbing is just of the time being and we are working on the improvement of the setup interface.

PS2. The webpage for this project is http://openconnectome.github.com/Rambo3D/

Instructions to compile and execute on a mac

Compilation

The below procedure works well on my Air running Mac-OS 10.7.4

1. Download and install Xcode if you don't have it yet: https://developer.apple.com/xcode/ Note that the latest Xcode seems not to come with GCC anymore (!!!). So you will need to do the following manually: Go to "Xcode->preference->downloads" and then click to install "Command Line Tools" After it's done, do "which gcc" to make sure it is there.

2. Download and install Qt SDK 1.1.2 (selecting "Mac 64" option, of course): http://www.developer.nokia.com/info/sw.nokia.com/id/84801bfe-8517-4287-9829-014c6f572127/Qt_SDK_1_1_2.html Yes, this is an older version. You could try the latest release instead (http://qt-project.org/downloads) but I haven't tested it out, so no guarantee...

3. Download and install GLEW as following:

   1. download and extract the package from https://sourceforge.net/projects/glew/files/glew/1.9.0/glew-1.9.0.tgz/download
   2. cd into the directory (doesn't matter where you extract btw)
   3. do "make install" (you may need to be a sudoer to do this)

4. Download and compile Rambo3D as following:

   1. download and extract the source code
   2. fire up "VolumeViewer.pro" by double-clicking
   3. click "Done" (you should see that the default selects the "Desktop" configuration)
   4. Compile the code by "Build->Build Project VolumeViewer" (or simply "Command+B")

Execution

1. cd into the directory where the binary was created (starting for the source code directory, usually it should be at: ../VolumeViewer-build-desktop/VolumeViewer.app/Contents/MacOS/)

2. Download and extract the attached "Supplementary.zip"

3. Copy everything to the binary directory

4. Run "./VolumeViewer --dRes 256 256 128 --img myImg.data --ano myAno.data"

5. Ta-da!!

--Ming