May 11, 2018 Software Open Access

Locating human splenic capillary sheaths in virtual reality - Supplementary material

Lobachev, Oleg; Steiniger, Birte S.; Berthold, Moritz

If you have a modern browser, you should be able to view the Videos and Tables online by clicking a link in the paper. The Supplementary Files need to be downloaded and unpacked completely beforehand. A modern graphics card is required for the interactive visualisation and for virtual reality application, it runs on Windows only. For other operating systems or if the application does not run, please install MeshLab to view the reconstruction. Press F1 in the interactive visualisation for help.

Files:

• Files File_S1.zip - File_S11.zip (for regions R1 - R11), File_S12.zip - File_S15.zip (for Figs. 4b,d, 5a,b) contain data sets for interactive visualisation. Download such a data set and extract the files from the zip file. On Windows: click on start.bat. The application launches automatically. If an eventual warning about an unsigned batch file appears, please allow the execution. The application will use a VR headset if present. A VR headset is not required, but recommended. See below or press F1 for short usage instructions.
• Files Table_S1.* and Table_S2.* provide supplementary tables to the text in various formats. Table S1 shows number and percentage of green and blue capillary sheaths. Table S2 lists iso-values used for different regions.
• Files Video_S1.mov - Video_S3.mov show a visualisation of data sets R1 to R3 as a video.
• File Video_S4.mov shows an interactive visualisation of region R1 and quality control in VR perspective as video.
• Files Video_S[1-4]_small.mov are smaller versions of above videos with reduced quality and size.

Abbreviations:

f: follicle; t: trabecula; tv: trabecular vein; v: vein.

Usage of interactive data sets:

• The file "start.bat" in the unpacked data from the zip file of a data set (file_sXX.zip) launches the application.
  • On a Mac or Linux use MeshLab to open mesh.ply in the data set. The text below assumes you use our viewer (start.bat).
  • If you have a functional graphics card, a window will appear with the interactive reconstruction display.
  • If you also happen to have a HTC Vive VR headset  connected, the same data set is also displayed in the headset.
  • We recommend to use VR immersion if possible.
  • Any other Steam VR-compatible headset (such as Oculus Rift) should work, too.
• In VR:
  • The motion of the user is used for navigation.
  • The red controller can be used to:
    • blend in the original sections (menu button),
    • page through them (top and bottom of the touchpad),
    • blend out the reconstructions (trigger).
  • The other controller (green) carries a ball that is used for annotations and further data analytics in the full version. The touchpad on the green controller changes the colour of the ball.
• Outside VR:
  • F1 for help
  • F2 for an overview with annotations
  •  use WSAD to navigate,
  • CV to move up/down,
  • mouse drag to turn,
  • + and - on the keypad to zoom,
  • I ("i" key) to turn the sections on and off,
  • JK to move sections,
  • E to blend the reconstruction out.
  • ESC quits.
• The VR Viewer application (bundled with the data sets) is licensed under the Unlicense, in other words it is in public domain. Please contact Moritz Berthold or Oleg Lobachev for a full version.

Main text:

These data are meant to supplement our paper "Locating human splenic capillary sheaths in virtual reality", Scientific Reports, volume 8, Article 15720 (2018).