Loading Volumes into Voxx2

To load volumes into Voxx2 right-click on the main window, and choose Volumes in the popup menu, then select Open Stack in the submenu. The open stack option is also available by right-clicking on the Stack Manager Window or by clicking on File, Load, Load Stack. This will prompt you for the first file in the dataset. After selecting the first file, you will be presented with the appropriate loader dialog for that file type. Please note if you are trying to load a sequence of individual tiff files, choose Load Sequence Tiff instead. Alternatively, if the combination of files is simple enough draging and droping the dataset onto Voxx2 main window will load it.

Voxx2 can open Biorad (.pic), Zeiss(.lsm), Metamorph(.stk), and many Tiff(.tif) file formats. If you encounter a file format Voxx2 cannot read, please share it with us. The microscopy facility allows us to generate many test datasets in many formats, but cannot cover every permutation. Given the many possible combinations of files, the loader dialog has been divided into two tabbed pages. Files which contain one color channel and one time point are loaded using the first (default) tabbed page. Multichannel files (like lsm) are loaded using the second page. After you select a tabbed page, simply click on the button next to where the filename goes, choose your file, and select open or select details for more options.

Clicking on the Details button will display a panel which allows you to choose which slices of the stack you want to load, with First Slice, Last Slice, and Step. Step allows you to load only every Nth slice for oversampled datasets. It often takes 40 or more slices to get a noticeable 3D effect. 80-120 slices works well for most situations, but we have had situations where 200-300 slices were necessary to produce a high-quality 3D effect. So don't undersample your image stacks.

If your video card supports 3D Texture Maps, you can choose between rendering with 2D and 3D texture maps. 3D texture maps consume 1/3 the memory of 2D texture maps but render slower. However, the main factor affecting speed is whether the whole volume will fit in the memory on the video card or not. So if by using 3D texture maps it will fit, you should see a performance improvement. The other advantage of 3D texture maps is they allow for Z axis reslicing (aka interpolation). This can help some with stacks with very few slices.

Finally, there is the Conserve Memory option. If selected, the original data will be dumped from memory after the volume is encoded. This eliminates a copy of the volume in memory. This copy is currently unused, but will be in the future for 3D image processing and quantitative work. Selecting it does not negatively impact rendering performance.

Time Series

If you want to load 4D data you must check the time series box and specify the file names by wildcards. I.e. if your files are foo01.pic, foo02.pic, foo03.pic and so on, you would specify foo*.pic. Remember this will load all file in the folder that match that description, so name your files wisely! Also, all of the volumes have to have the same number of channels/slices/bitdepth, etc.