semviewer: Scanning Electron Microscope Data Viewer

A three.js based web application that displays scanning electron microscope data. Demo

Run locally

• Unzip sample files

gunzip output.nrrd.gz
gunzip my.obj.gz

• Run a web server locally to serve output.nrrd and my.obj files

#install (it requires nodejs/npm)
npm install http-server -g

#run
http-server -p 8080 --cors

• Open localviewer.html in a browser

• Open mesh.html in a browser

Run in Docker container

• Build container and run

docker build -t semviewer .
docker run -p 8080:8080 semviewer

• Open http://localhost:8080 in browser

GCloud Deployment

gcloud auth login
gcloud builds submit --tag gcr.io/[PROJECTID]/semviewer
gcloud run deploy --image  gcr.io/[PROJECTID]/semviewer

Notes

• To create nrrd file from a set of png files use png2nrrd.py. Update datapath and correct the header as below.

• Sample NRRD header that Three.js can read

NRRD0004
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: short
dimension: 3
space: left-posterior-superior
sizes: 1000 1000 100
space directions: (0.93750000000000022,0,0) (0,-0.93750000000000022,0) (0,0,-1.5000000000000004)
kinds: domain domain domain
endian: little
encoding: ascii
space origin: (-119.53000000000002,119.53000000000007,84.000000000000028)

• Response size limit is 32MB in google cloud run. Hence large nrrd files cant be served from container.

Links

• Eyewire neuron mesh samples