ChimeraX-measure-intensity

Steps to measure intensity of surface

1. Generate the KDtree from nonzero points in 3D image
2. Query the KDTree with a given radius (r=15)
3. Calculate intensities from the queried radius
4. Normalize the intensity to the mean

The initial profiling (of similar meSPIM code) in Matlab took ~15 minutes to complete with the majority of time spent querying KDTree. Once the refactoring was complete, this reduced this to ~3 seconds.

Usage

Clone the repo and install in ChimeraX

gh repo clone bscott711/ChimeraX-measure-intensity
cd $Repo_dir
devel build . ; devel install . ; devel clean . ;

If Needed Remove the Old.
toolshed uninstall measure-intensity

Download the demo data to X:\Demo_data: Demo Data

Run the following commands in ChimeraX

cd X:\\demo_data\\
open X:\\demo_data\\*ch0_*.tif format images
open X:\\demo_data\\*ch1_*.tif format images
open X:\\demo_data\\*ch2_*.tif format images
volume #1.1 level 46 style surface
volume #2.1 style image maximumIntensityProjection true level 0,0 level 192,1 level 1260,1
volume #3.1 level 31 style surface
measure intensity #3.1-5 toMap #2.1-5 range 0,5
measure distance #1.1-4 toSurface #1.2-5 range 0,40
surface recolor #1 metric distance palette spectral range 0,30

Representative Intensity

Initial Isosurfaces	Secondary Intensity	Surface Intensity

Representative Distance between Time=x and Time=x+1

Initial Surfaces	Distance in next frame	Distance and Intensity

Create interactive surface

1. Save surfaces in GLB format
2. DRACO compress with optimized settings
3. Upload files for display in Babylon.JS

ChimeraX commands to run

hide #!1-3 models;
perframe "show #!1,3.$1 models; wait 1; save Surfaces_$1.glb floatColors true; wait 1; hide #!1,3.$1 models; wait 1;" ranges 1,5

Ensure gltf-pipeline is installed and on the PATH. Run in the cmd prompt

cd X:\\demo_data\\

This will save the file in the subdirectory draco with the same name.
for /F %x in ('dir /b *.glb') do (gltf-pipeline -d true -i %x -o ./draco/%x)

Use the following for a maximally compressed gltf.
for /F %x in ('dir /b *.glb') do (gltf-pipeline -i %x -o ./draco/%x -d true --draco.quantizePositionBits 10 --draco.quantizeNormalBits 5)

If MParallel is installed you can gain a 5x speed increase: MParallel

cd X:\\demo_data\\

Run the Draco compressed batch file in the new directory.
$Repo_dir\draco_compressed.bat

Compression results

Surface ID	Raw GLB (KB)	Draco Compressed (KB)	Compression Ratio X
Surface 1	28,922	1563	18.5
Surface 47	42,248	2305	18.3

Update to using a more advanced compression algorithm that includes mesh simplification

There is no perceptual difference between the meshes, but the file size tells us there is a difference, and the loading time does as well.

Install Gltf-Pack
npm install -g gltf-pack

cd X:\\demo_data\\

Use the following for a simplified and maximally compressed gltf.
if not exist ".\draco" mkdir ".\draco"
for /F %x in ('dir /b *.glb') do (gltfpack -i %x -o .\draco\%x -cc -tc -kn -si 0.5 -vp 10 -vt 10 -vn 5)

The same can be done using MParallel

cd X:\\demo_data\\

Run the Draco compressed batch file in the new directory.
$Repo_dir\draco_pack.bat

Compression results for gltf-pack

Surface ID	Raw GLB (KB)	Draco Compressed (KB)	Compression Ratio X
Surface 10	31,145	1538	20.25
Surface 130	44,943	2491	18.04

If the files need renamed, you can do that using Powershell

Move into the folder and run the following: Get-ChildItem *.glb | Rename-Item -NewName { $.Name -replace 'Surfaces','Eat_' }

The first string is the original file name and the second string will be what it is replaced with It is recommended to have an underscore before the number so that is all that changes as it is indexed