Deliverables for November 28th

NeuroDataDesign / seelviz-f16s17

Undergraduate repository for Albert, Luke, and Tony

Apache License 2.0

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Deliverables for November 28th #49

Closed mlee156 closed 7 years ago

mlee156 commented 7 years ago

committed

status	deliverable	notes
🐉	Code.md for connectivity algorithm	@lukezhu1 https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/Jupyter/Connectivity_codemd.ipynb
🍙	A registered brain to Allen atlas ingested into ndstore, with ndviz link showing the brain overlaid with the Atlas	http://viz.neurodata.io/Aut1374_albert/# @alee156 @toekneesunshine
🍙	Make output webpage have links to everything pertinent	http://cortex.jhu.edu:8900/ @jonl1096

reach

status	deliverable	notes
:x:	Ingest the ARA as a RAMON object so that you can see the names of each region	@lukezhu1
:x:	Ingest 100,000 brightest points and overlay them on both views of the brain	@toekneesunshine
:x:	Figure out how to deal with hierarchical atlas - deliverable is jupyter notebook with our work	@jonl1096 ipynb html
:x:	Provide detailed instructions for how to best generate manually labeled data for tracing processes	@lukezhu1

mlee156 commented 7 years ago

@gkiar @jovo Just realized that for some reason my tag didn't submit when I made the issue last week ... my bad

jovo commented 7 years ago

different histogram equalization code won't solve hierarchy problem. also, please don't link to this issue, that is not useful for anybody. otherwise, looks good.

jovo commented 7 years ago

@toekneesunshine

[ ] have you seen @kkutten1 version of ingesting these? let's talk to him about this.
[ ] let's get @kkutten1 to be on this team?
[ ] look at @kkutten1 most recent notebook

@jonl1096

[ ] let's look at the actual hierarchy, not the brain, see if you can plot the ARA using whatever for the different levels of the hierarchy

@lukezhu1

[ ] do algorithms.md for realz yo.

02agarwalt commented 7 years ago

@jonl1096 for the ipynb, it might be more helpful for viewers if you include some more graphics for the simulations, kind of like in algorithms.md. Right now its mostly consecutive blocks of code which aren't very clear. Some written explanations/overviews would be helpful too.

rmarren1 commented 7 years ago

the website on cortex links to the website on github pages, then you can't get back. maybe the links need to fixed if that isnt on purpose

mnatenz1 commented 7 years ago

@lukezhu1 None of the plots you made for the connectivity algorithm.md are working

mlee156 commented 7 years ago

jupyter notebook rendered plots don't work on github five minutes ago, we are trying to fix it now.

kkutten1 commented 7 years ago

@toekneesunshine: If you want to talk about image registration let me know