Changes between Version 48 and Version 49 of NIAID2022


Ignore:
Timestamp:
Jan 26, 2023, 3:07:18 PM (3 years ago)
Author:
Tom Goddard
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • NIAID2022

    v48 v49  
    6767This time we can just extend the existing contract, but with a new SOW.
    6868
    69 DICOM - Scooter: continue work, with areas including handling more diversity of datasets/datatypes; segmentation; presets (windowing, lighting, transparency handling). Darrell: we appreciate the ChimeraX rendering and being able to manipulate fairly large data without stuttering. At the same time we don't want to duplicate Slicer, or only support tools we ourselves would use... we want to benefit the larger research community.  Phil: would like easier ability to set windowing/leveling in VR, especially of complex presets with multiple peaks/colors. Just making the Volume Viewer histogram a lot bigger may help. TomG: you can do it with any tool in VR by clicking both controllers' panel-showing buttons at the same time and dragging apart. Everybody: wow, didn't know that!
     69DICOM - Scooter: continue work, with areas including handling more diversity of datasets/datatypes; segmentation; presets (windowing, lighting, transparency handling). Darrell: we appreciate the ChimeraX quality of rendering and being able to manipulate fairly large data without stuttering. At the same time we don't want to duplicate Slicer, or only support tools we ourselves would use... we want to benefit the larger research community.  Phil: would like easier ability to set windowing/leveling in VR, especially of complex presets with multiple peaks/colors. Just making the Volume Viewer histogram a lot bigger may help. TomG: you can do it with any tool in VR by clicking both controllers' panel-showing buttons at the same time and dragging apart. Everybody: wow, didn't know that!  TomG: Enhancing windowing/leveling vr mode to show visual heads-up display of histogram and curve would make it easier to use.
    7070
    7171NIH3D - put all pipeline-associated code on github. Eric: is already on github.  Scooter: maybe needs to be more evident/obvious.  Darrell: may just be for NIH3D website to add a link(s) if you let ue know what they are.  Also, make sure relevant bundles on Toolshed are amply documented there.  Scooter: we can add the usual "continue to support NIH3D pipeline" to cover any other needs that arise.
    7272
    73 Scooter: what can we do to support/promote use of your visualization wall? Meghan: so far the networking aspect has occupied us, rather than the content of the display.  Scooter: may need to handle menuing differently, for example.  Maybe as you get more experience with it, please do give feedback on interface issues. Eric: and for selection, rather than Ctrl-click... Darrell: the wall is multitouch. Also it's not just extra-large but ultrawide. Phil: need to check out how it works with tiling. TomG: the multitouch might already work in some capacity.
    74 
    75 Greg: is anybody getting one of those Aces (?) monitors with autostereo? Scooter: reviews have not been that good.  We could purchase a widescreen monitor to investigate some of these issues. Meghan: speaking of hardware, could you get a Quest Pro with passthrough video? We have two. Allows all to see each other in VR, not as "Picasso heads." (something I didn't catch about having to wear blinders to block out surrounding light) TomG: depth-sensing can be tricky with these cameras.
     73Scooter: what can we do to support/promote use of your BioVis Lab visualization wall? Meghan: so far the networking aspect has occupied us, rather than the content of the display.  Scooter: may need to handle menuing differently, for example.  Maybe as you get more experience with it, please do give feedback on interface issues. Eric: and for selection, rather than Ctrl-click... Darrell: the wall is multitouch (infrared plane). Also it's not just extra-large but ultrawide. Phil: need to check out how it works with tiling. TomG: the multitouch might already work in some capacity.  Meghan: Yes, some multitouch does work with ChimeraX on wall.  TomG: Might use extra wide display to show multiple independent camera views.
     74
     75Greg: is anybody getting one of those Acer laptop monitors with autostereo? Scooter: reviews have not been that good.  We could purchase a widescreen monitor to investigate some of these issues. Meghan: speaking of hardware, could you get a Quest Pro with passthrough video? We have two. Allows all to see each other in VR, not as "Picasso heads."  Quest Pro already lets you see room in peripheral vision if blinder attachments not used. TomG: depth-sensing can be tricky with these pass-through cameras, maybe room video is placed always behind computer generated objects.
    7676
    7777Scooter: also on the list, exporting a ChimeraX session for Quest2 VR (as detailed in email from TomG 1/25/23)
    … …  
    8181Darrell: keep level of effort about the same as last year.
    8282
    83 Phil: maybe this falls under NIH3D umbrella, have you heard anything more from Enduvo?  TomG: no. Phil: I need to contact them soon, will prod them about this.  TomG: was using 2.6.0 experimental version, with gltf warnings... lack of colors may relate to that, maybe they are not supporting gltf well.  Phil: they "support" many formats but level of support may not be very high. I could get surfaces of different colors but other things like ribbons were white.  TomG: each surface is a single color, though. So Enduvo can show single color per object. ChimeraX ribbons use vertex colors, not single colors, which is come up as white in Enduvo. Phil: Enduvo may not handle vertex colors regardless of format.
     83Phil: maybe this falls under NIH3D umbrella, have you heard anything more from Enduvo?  TomG: no. Phil: I need to contact them soon, will prod them about this.  TomG: was using Enduvo 2.6.0 experimental version, with gltf warnings... lack of colors may relate to that, maybe they are not supporting gltf well.  Phil: they "support" many formats but level of support may not be very high. I could get surfaces of different colors but other things like ribbons were white.  TomG: each surface is a single color, though. So Enduvo can show single color per object. ChimeraX ribbons use vertex colors, not single colors, which is come up as white in Enduvo. Phil: Enduvo may not handle vertex colors regardless of format.  TomG: Could enhance ChimeraX GLTF output to use single colors and separate objects.
    8484
    8585Kristen: one open issue for NIH3D, not showing zinc atoms #8218.
    8686Eric: again an EBI assembly file for NMR structure. Greg: something about disjoint sets of atoms?  TomG: works in daily build.  Greg: was same problem as another ticket that has been fixed.  Will close ticket.
    8787
    88 Meghan: haptic feedback on hydrophobic/hydrophilic or ESP? Elaine: need something with a gradient, and also we don't have a full interaction energy calculation (e.g. no VDW/steric component), so it wouldn't be very helpful for manual ligand docking.  Maybe fitting atoms into density?  TomG: this is just a vibration, not a force, so may not be very helpful/intuitive.  Scooter: maybe number of contacts/clashes could translate to strength of vibration.  Eric: will have to see if the continually updating clashes would slow down VR rendering.
     88Meghan: haptic feedback on hydrophobic/hydrophilic or ESP? Elaine: need something with a gradient, and also we don't have a full interaction energy calculation (e.g. no VDW/steric component), so it wouldn't be very helpful for manual ligand docking.  Maybe fitting atoms into density?  TomG: this is just a vibration, not a force, so may not be very helpful/intuitive.  Scooter: maybe number of contacts/clashes could translate to strength of vibration.  Eric: will have to see if the continually updating clashes would slow down VR rendering.  TomG: VR haptics useful for toolbar button clicks and user interaction cues.
    8989
    9090Darrell: maybe SOW could say "investigate utility of haptics" and maybe it could be part of a paper on pedagogical benefits of VR.  Darrell: if some type of haptic feedback is associated with popular VR hardware, more people would have it.  Whereas something like Phantom with a more complete haptic interaction is expensive and very few users would have access.