Deliverables For Final Presentation

[toekneesunshine]

Remainder of year:

@alee156

• [x] official jovo pitch with brightest points for new ailey brain Slide deck for Jovo pitch current iteration for final project ########Reach#########
• [x] Work on tractography -> Try to convert (https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/AlbertImages/tract.md)

@jonl1096:

• [x] get batch simulation to work ipybn
• [x] integrate tony's centroid code into pipeline ipybn

@toekneesunshine:

• [x] integrate centroids calculation into pipeline
• [x] obtain and run results of pipeline with results from s3617 (outputs here)
• [x] try to fix tractography script (see above visualizations). Fixed: overflow bug (since old inputs didn't overflow), reordered script to follow CAPTURE Github, rewrote most of this to get it to match up and work. Works with 95% accuracy on the sample data in Python, tested here using sample outputs they provided.
• [x] Properly load the brain stack (previous error was fixed, now properly loads brain stack in right order after sorting inputs). Latest scripts.

@lukezhu1:

• [x] get medial view of brain brain
  • [ ] get side-by-side medial views of both hemispheres
  • [x] apply opacity-scaling to indicate intensity/activity of brain region notebook plotly

Other:

• [ ] Finalize web service hosting to allow user input to send stuff to Batch (plus documentation on how to set it up / requirements).
• [ ] Batch with pipeline sending stuff to S3 with the proper buckets for input/output (plus documentation about which Docker container was used, how S3 was configured, how to configure the setup files).
• [ ] Visualization of centroids of activity scaled by volume, ipynb documenting proof (qualitatively showing corresponding region of raw data).
• [ ] Visualization of regions of brain as mesh grid, with activity either scaled by opacity or some other way, ipynb documenting proof (again can be qualitatively showing corresponding region of raw data).
• [ ] Connectivity estimate of different regions of brain and confidence of connectivity estimate (plus documentation explaining how we generated this connectivity estimate/confidence)
• [ ] Documentation for older functions updated to reflect any changes (link ipynb for each function inputs/outputs)

[mlee156]

For May 8th 2016 @alee156

• [x] Generate fibers and show to Jovo (https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/Albert_Jupyter/brain1.png)
• [X] Fixed bug where tract viz didn't work (https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/Albert_Jupyter/connectomes%2Bfinal.ipynb)
• [X] New draft of presentation (https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/ndd.pptx.pdf)

@jonl1096

• [x] Finish batch and submit it

@lukezhu1

• [x] Connectivity based off of Jovo feedback connectivity comparison with spectral embedding
• [ ] 2D projection of mesh to indicate active vs non-active regions
• [ ] combine Tony's centroid plot with opaque 3D mesh

@toekneesunshine

• [x] Fix various bugs and implement tract into pipeline.

[mlee156]

https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/Albert_Jupyter/newest/tensors-test-graph.ipynb