Changes between Version 13 and Version 14 of NeteSOW

Timestamp:

Sep 24, 2020, 2:52:51 PM (5 years ago)

Author:

Tom Goddard

Comment:

--

NeteSOW

@@ -5 +5 @@
 1. Extensions to ChimeraX to support the NIH 3D pipeline
    a. Support the conversion of existing NIH 3D Print Exchange Chimera scripts to ChimeraX, advising on ChimeraX syntax for capabilities where available and noting missing features in ChimeraX where comparable features don’t exist
+     i. **Investigate using Smart Display**
+     i. **Discuss Python vs. ChimeraX command line**
    a. ~~Implement essential missing features discovered above, including:
       i. ~~!PubChem fetch
@@ -11 +13 @@
    a. ~~Sequence conservation coloring in ChimeraX
    a. Fetch sequence annotations (!UniProt, domains, disease-associated mutations) (Eric)
+      i. Automatic labels
    a. Enhancements to X3D export format (Greg)
+      i. Look at GLTF export improvements (support for both per vertex coloring and **texture coloring**)
    a. Read and visualize segmentation models (see deliverable 2) (Tom)
+
 2. Significantly enhance ChimeraX’s segmentation capabilities for 3d electron microscopy, light microscopy, and medical imaging
    a. Interactive SimpleITK use in ChimeraX (Tom)
    a. Allow loading, visualizing, creating, measuring and saving segmentations. (Tom)
    a. Support new EMDB-SFF segmentation file format from the EM Databank (Tom). #3639 in progress
+   a. NOTE: some example data sets would be useful - AI Detected Lesions in lungs.  Phil will get some data to TomG.  Could also look at some data sets from SimpleITK.  Bryan Hansen and Beth Fisher could also get some data sets
+
 3. Medical imaging
    a. Metadata browser for DICOM files (Tom)
-   a. Support radiologist collaborator needs by adapting ChimeraX to better suit standard workflows and to provide critical missing features identified by our collaborators (Tom)
+   a. **Support radiologist collaborator needs by adapting ChimeraX to better suit standard workflows and to provide critical missing features identified by our collaborators** (Tom)
       i. Need to get a collaborator
-      i. Roberto Rodriguez Rubio, MD at UCSF director of [https://skullbaselab.ucsf.edu Skull Base lab], interested in VR.
+      i. Les Folio / Ron Summers
+      i. New NIAID section focused on lung imaging
+      i. Roberto Rodriguez Rubio, MD at UCSF director of [https://skullbaselab.ucsf.edu Skull Base lab], interested in VR.  Emphasis on dissections, no medical imaging.
+
 4. Improve multi-person VR beyond work accomplished in 2019 SOW
-   a. Localizable connection server solution - deliver a rendezvous server that can easily be deployed by institutions or enterprises. (Conrad/Greg)
+   a. **Localizable connection server solution - deliver a rendezvous server that can easily be deployed by institutions or enterprises. (Conrad/Greg)**
       i. Fix cxconference TLS security #3629
       i. Get TLS certificate for plato cxconference server (Greg)
@@ -44 +54 @@
 1. Adding Coulombic coloring (Eric) #3596 (Elaine: this is one of the essential missing features mentioned in 1b above)
    a. 90% cases covered
-2. ~~Adding support for SDF V3000 (Eric)
+1. Colada import/export
+1. ~~Add support for SDF V3000 (Eric)