[bicubic]

Do you know where I could source some sample data? I'm developing a VR data visualization system but not in this particular context, could certainly look into it.

[cake93]

Here, follow the instructions to download and install the HDF5 plugin for Fiji:

http://lmb.informatik.uni-freiburg.de/resources/opensource/i...

From the same site you can download "pollen.h5". Then follow the steps to load the dataset in "hyperstack (multichannel)" mode. This will open a window where each frame in the movie is a z-slice of the 3D image.

Then go to Plugins/Volume Viewer (scroll down) and switch the mode (top left) to "Volume". (this is what you should get: http://i.imgur.com/0QoGa1t.png)

The same people also published lots of 3D data of the zebrafish embry. Have a look at:

http://vibez.informatik.uni-freiburg.de/

Look for "e098.h5" to download it.

If you have never worked with the HDF5 format before, you can use HDF5 View (https://support.hdfgroup.org/products/java/hdfview/) to look into the files. As you can see here (http://i.imgur.com/nnTiyQh.png) the data in pollen.h5 basically is a uint8-array of 193x199x419.

There are libraries for many languages to read HDF5. Eg. "h5py" for Python.

[bicubic]

Thanks for the references, looking.

By the way, check out https://www.youtube.com/watch?v=-PVAcLlYUpg

[billconan]

This is Cool!

[cake93]

[follow up]

For Light Sheet 3D video of developing fly embryo take a look here: http://www.digital-embryo.org/ They have movies and also downloads of the raw data and Matlab pipline for analysis.

Notice that this was published in 2012. Fresh data doesn't get published before the analysis is done and the paper written..

[billconan]

Is this volumetric data?

[cake93]

Yes.

These are images taken by confocal microscopy, where you focus a laser scanning microscope on a plane and only see that. Then you move the focus plane up by a bit and take the next picture.

Super-resolution microscopy such as STORM, STED or PALM on the other hand will give you coordinates.