October 5, 2016

Deliverables

Individual Tasks:

Jon:

• [x] Complete pipeline and make Python package. Pipeline code should be pip installable.
• [x] Provide evidence that the pipeline works. Testing here.
• [x] Complete documentation and organize Github repository

Luke:

• [x] Create Docker for pipeline with Albert once pipeline is complete

Tony:

• [x] Addressed Davi Bock's issue - make a plotly plot of Cocaine174 where voxels are colored according to component size.
  • Jupyter Notebook containing a generalized Plotly plotting script for density.
  • Deliverable was to apply it to Cocaine174 using ball size of 25, to color the voxels according to component size. Here is a 5000 point downsampled version I made initially (verified accuracy by finding max brightness values and comparing them to the node values on the chart). Here is the 40k node false color version I made. I also checked the maximum brightness value and compared it to the brightness I got by scanning the list.
  • For cross referencing, made a heat map coded for each 5%; shown here is the corresponding edge to color mapping for the downsampled Cocaine174. Here is the corresponding edge to color mapping for the full scale Cocaine174 plot.

Albert:

• [x] Create Docker for pipeline with Luke.
• [x] Set up package page for prototype with installation instructions. Build passes on travis-ci.

Group Task for Albert, Luke, Tony:

Show the 40,000 brightest points in registered space relative to the registered region. Tasks as follows:

Albert:

• [x] Downsample or obtain atlas and one raw image so that they are less than 2 GB in size
  • Learned from Kwame how to downsample effectively using "spacing".
  • https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/miniatlas.nii
  • https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/Ndreg%20Simple%20Downsampling%20Method.ipynb
• [x] Write code for aligning atlas to the raw images instead of other way around:
  • https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/ReverseAlignmentDownsampled.ipynb
  • https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/albert/brainalign.py
  • https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/albert/reverse_affine_annotations.png
• [x] Write code used for resolution 5 images on server
  • https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/albert/brainalign.py

Luke:

• [x] Run code on resolution 5 images using server
• [x] Create plotly plot representing each region of the brain as a different color
  • https://neurodatadesign.github.io/seelviz/reveal/html/graphmlhtmls/Control258localeq.region_color.html
• [x] Sum intensity in each region
  • https://neurodatadesign.github.io/seelviz/reveal/html/Control258localeq.region_activity.html
  • https://neurodatadesign.github.io/seelviz/reveal/html/Control258localeq.region_activity_blackbg.html

Tony:

• [?] Create plotly plot of graphml network on new brain
  • Jupyter notebook code for raw graphML to 3D plot with edges.
  • Control258 40k nodes.
  • Aut1374 100k nodes.
    • Need the new raw .nii file for Aut1374, this graphml was still captured from the old .nii
    • Data not fully propogated for Aut1374 new brain (or propagated properly)
• [x] Setup server and install all packages
  • Procured and setup a Google Cloud instance (similar to an Amazon AWS EC2 instance) free trial with $300 credits.