Changes between Initial Version and Version 1 of MSCContract

Timestamp:

Feb 14, 2019, 12:18:53 PM (7 years ago)

Author:

Tom Goddard

Comment:

--

MSCContract

@@ +1 @@
+= Medical Science Computing contract Ideas =
+
+Feb 13, 2019
+
+== Background ==
+What developments should we propose for a March 2019 one year subcontract with
+Medical Science Computing?  Meghan !McCarthy and Darrell Hurt say it can be broader
+than medical imaging and VR.  Meghan mentioned next gen NIH 3D print exchange
+including VR/AR with those models and in-browser visualization (specifically the
+WebXR preliminary standard) and tutorials.  She also mentioned cytoscape 3d and VR viz.
+Darrell said though that the focus should be VR.  There was some discussion of the
+NIAID interest in vacine development and molecular visualization and analysis.
+
+== General Considerations ==
+
+Should we propose new areas like web VR or augmented reality or machine learning?
+
+VR has uses for demonstrations, collaboration, and analysis.  Where should we focus?
+
+ChimeraX has VR capabilities for molecular structure, electron microsocopy, optical
+microscopy, medical imaging.  Which application area should we focus on?
+
+ == Relation to our other VR projects ==
+
+What do I want to do with VR in the next year?  Would like to move it beyond
+demonstrations, advance its use for collaboration an analysis in other labs.
+The main ingredient needed is collaborators with specific problems.  Maybe the
+most promising chance for that is in cryoEM atomic model building with Yifan
+and Adam.  I need to get Dyche and Max Krummel setup up for optical microscopy VR.
+Also I have more to do on binding site VR for Koda-Kimble award.  MSC does not
+have end-users so they are not the collaborators.  Proposed projects need specific
+collaborators who will be using the tools.
+
+== What does NIAID want? ==
+
+An key missing part of the picture is what exactly the MSC contract from NIAID
+is funding.  A subcontract would of course need to be aligned with the goals of
+the primary contract.  If we don't know those details then we may propose things
+that are not in the scope of what can be funded.
+
+== Interesting application areas ==
+
+=== Segmentation using VR ===
+
+Use [http://www.simpleitk.org Simple ITK] in ChimeraX.  [wiki:HurtITK Darrell Hurt says] NIAID has hired SimpleITK team
+      
+Slicer [https://www.youtube.com/watch?v=BJoIexIvtGo&feature=youtu.be grow from seeds] segmentation, cardiac CT
+      
+
+Slicer [https://www.youtube.com/watch?v=0at15gjk-Ns&feature=youtu.be scissor projection tool], masking to sphere (volume eraser) for hip ball joint
+      
+
+Machine learning segmentation methods for medical images and [https://www.allencell.org/label-free-determination.html cell microscopy]. Need to investigate medical imaging methods that could be used
+
+Segger watershed segmentation, especially hand mode used with [http://www.cgl.ucsf.edu/chimera/data/ncsm-nov2012/microscopy.html termite gut].
+
+Tools to adapt to VR:
+   - Volume eraser
+   - Hide dust
+   - Show only largest connected blobs
+   - Loop tracing
+   - Masking to surface to create binary segmentation
+
+=== Building molecular models in cryoEM using VR ===
+
+ - ISOLDE in VR
+ - Rotamers
+ - Build structure
+ - Clashes
+ - OpenMM and MD tools
+   * parameterization
+   *  charges
+ - Interactive local energy minimization
+
+=== NIH 3D ===
+
+3D printing needs
+  - Color printing format requirements
+   - Reduced level of detail controls
+
+Web VR visualization
+  - Primarily for communication and education
+  - AltPDB.  ChimeraX exports glTF scene used with !AltSpace to provide Web VR collaborative molecular PDB display (ribbons, surfaces, atoms).
+  - [https://www.stevenabbott.co.uk/practical-solubility/Peptides-VR.php Peptide solubility Web VR app]. Solid phase protein synthesis, Steve Kent, Steven Abbott
+         
+ - Could ChimeraX offer web browser connection for multiperson VR viewing-only mode?  Or just export to an AltSpace or other social VR site with one button click?
+
+=== Medical and optical image visualization ===
+
+ - [https://www.allencell.org/photorealistic-cells.html Photorealistic lighting] from Allen Cell Science.
+      
+  - Presets for coloring [https://en.wikipedia.org/wiki/Hounsfield_scale#Value_in_parts_of_the_body different tissues]   
+    * Horos
+ - Smart initial coloring (bones, different organs or tissue types)
+ - Machine learning to [https://www.allencell.org/label-free-determination.html color organelles in cells]. [https://www.alleninstitute.org/what-we-do/cell-science/news-press/press-releases/machine-learning-technique-predict-human-cells-organization-published-nature-methods Video].
+       
+       
+
+=== VR training ===
+
+Mixed reality video capture shows person and data.
+    - For tutorials and explaining research results to public.
+
+How-To screen capture videos
+
+Multiperson VR sessions for remote training, possibly group training.
+
+=== Multiperson VR ===
+Remote and same room collaborative VR discussions.
+
+Allow any participant to bring in new data.
+
+Task specific user interfaces
+  -  Drug binding analysis user interface
+  - Medical imaging
+  - Optical microscopy
+  - cryoEM modelling