neurodata/nshack17

Neurostorm Hackathon (2017 @ MBL)

See the wiki for administrative details.

Project ideas are under projects. Create an issue if/when you want to start working on an item!

Mini-tutorials are under issues. Please up vote what you have interest in, and reply if you are a knowledgable source!

Writeup! We need 1-2 sentences on what you accomplished and affiliation. Add to overleaf or send to Greg or JoVo!

nshack17's Issues

ingest zbrain masks

give @fcollman repo permissions

Ingest2NeurodataBoss

Automatic tracing of long range connections

Cell detection

Visualization

develop a hierarchical render based alignment workflow

Updated version of render image in AWS

Update the Docker instance(s) behind https://render-dev-eric.neurodata.io/render-ws/view/stacks.html .

Dockerize FEM tools for comparison of FEM mesh generation pipelines.

We would like to dockerize fijee, iso2mesh, SimNIBS, forward and BioFEM. The most recent stable versions of each tool will be used and as best as possible we should use matching versions of CGAL, Gmsh, meshfix and other mesh libraries that are common dependencies across the pipelines. Several datasets will eventually be used for comparison but the initial dataset would be the OpenFMRI ds0117 which is Rik Henson's multimodal dataset which includes T1, T2, DWI and EMEG electrophysiology data.

BIDS

Boss tilesource

Boss docs:

https://docs.theboss.io/docs/cutout-get

CATMAID tile source docs:

http://catmaid.readthedocs.io/en/stable/tile_sources.html

Stalled on:

• Requires authorization header
  • DOM tile layer
  • Pixi tile layer
  • 3D viewer
  • Backend

Docker

Web app project page

Z Brain github page
https://github.com/OnyekaN/Z-Brain-2

Render to BOSS

Convert render stacks to BOSS using ingest_large_vol.

• Given a owner/project/stack, scrape metadata for render for sides
• Generate slabs by querying render for data.

Initial version should allow thresholding on the command line for 16 to 8 bit conversion. A few tweaks to render will be needed to get 16-bit data out.

Skeleton export API in neuroglancer format

• Add a skeleton export for neuroglancer's binary format
• What does neuroglancer need to discover, enumerate and pull skeletons from a CATMAID server?

Ingest BigBrain

pipeline for ingest to BOSS from render

Alignment

Ingest Zbrain

Boutiques

Update movedata.py and move it into render-python-tools.

Update the existing movedata.py to:

• Copy masks
• Copy reference transforms (using getResolvedTiles?)
• Fix double slashes (//) in URLs
• Other metadata? (like Cycle/Step?)