{"action":"created","issue":{"url":"https://api.github.com/repos/NeuroDataDesign/seelviz/issues/26","repository_url":"https://api.github.com/repos/NeuroDataDesign/seelviz","labels_url":"https://api.github.com/repos/NeuroDataDesign/seelviz/issues/26/labels{/name}","comments_url":"https://api.github.com/repos/NeuroDataDesign/seelviz/issues/26/comments","events_url":"https://api.github.com/repos/NeuroDataDesign/seelviz/issues/26/events","html_url":"https://github.com/NeuroDataDesign/seelviz/issues/26","id":185848002,"number":26,"title":"October 31st Deliverables","user":{"login":"alee156","id":14059912,"avatar_url":"https://avatars.githubusercontent.com/u/14059912?v=3","gravatar_id":"","url":"https://api.github.com/users/alee156","html_url":"https://github.com/alee156","followers_url":"https://api.github.com/users/alee156/followers","following_url":"https://api.github.com/users/alee156/following{/other_user}","gists_url":"https://api.github.com/users/alee156/gists{/gist_id}","starred_url":"https://api.github.com/users/alee156/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alee156/subscriptions","organizations_url":"https://api.github.com/users/alee156/orgs","repos_url":"https://api.github.com/users/alee156/repos","events_url":"https://api.github.com/users/alee156/events{/privacy}","received_events_url":"https://api.github.com/users/alee156/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":14,"created_at":"2016-10-28T06:25:06Z","updated_at":"2016-11-01T00:27:36Z","closed_at":null,"body":"@alee156 @lukezhu1 \r\n- [x] Fix bug in backend where web app doesn't threshold app properly\r\n  - Deliverable is showing that not only two corners of the brain are visible in the plotlys\r\nhttps://github.com/NeuroDataDesign/seelviz/blob/gh-pages/reveal/html/Aut1367reorient_atlas.region_region_color.html\r\nhttps://github.com/NeuroDataDesign/seelviz/blob/gh-pages/reveal/html/Aut1367reorient_atlas_brain_figure.html\r\nhttps://github.com/NeuroDataDesign/seelviz/blob/gh-pages/reveal/html/Aut1367reorient_atlas_edges_graphml.html\r\nhttps://github.com/NeuroDataDesign/seelviz/blob/gh-pages/reveal/html/Aut1367reorient_atlasplotly.html\r\n- [x] Allow user input for orientation parameters\r\n  - Deliverable is web service shown to Jovo\r\n- [x] Modify input for functions such that we convert user inputted data into standardized form\r\n  - Deliverable is showing output for both nifti image and numpy array from ndstore are the same for our web service\r\n^ The links above are using token input, while jon's uses nifti input\r\n\r\n**Note: may not be bug**\r\n\r\n@jonl1096 \r\n- [x] Make backend for secondary page\r\n  - Deliverable is html of second page\r\n  - http://104.199.117.195/clarityviz/\r\n  - token: Aut1367reorient_atlas\r\n- [x] Make output of web service an html formatted \"report\" containing all the embedded plotly's in an organized fashion with table of contents\r\n  - Deliverable is output for Ailey's brain\r\n- [x] Time pipeline, and keep track of the specific order of steps\r\n  - Deliverable is a latex document with the time and order of steps\r\nhttps://github.com/NeuroDataDesign/seelviz/blob/gh-pages/Jupyter/Pipeline_Analytics.pdf\r\n\r\n@toekneesunshine \r\n- [x] Run sufficient number of trials on Ilastik until objects are clearly defined\r\n  - Deliverable is Jupyter notebook with justification for number of trials and outputs\r\n  - https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/Tony/Ilastik%20on%20Raw%20and%20HistEq%20Fear199%20Data.ipynb\r\n- [x] Run sufficient number of trials on histogram equalized brain until objects are clearly defined\r\n  - Deliverable is Jupyter notebook with justification for number of trials and outputs\r\n  - https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/Tony/Ilastik%20on%20Raw%20and%20HistEq%20Fear199%20Data.ipynb\r\n- [x] Afterwards type up report on findings in Latek\r\n  - Deliverable is Latex report\r\n  - Writeup talks about pretty much the exact same thing as the Jupyter Notebook linked above.  Since classifier didn't generate any objects in new data, just analyzed the training input data objects.  https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/pdfs/writeup-detailing-ilastik.pdf\r\n- [x] Type up report on findings in Latek describing the various algorithms we used for processing Ailey's brain and the rational behind them -> use this to interpret our results\r\n  - Deliverable is Latex report\r\n  - https://github.com/NeuroDataDesign/seelviz/blob/gh-pages/pdfs/clarityviz-algorithms-writeup.pdf\r\n\r\n@gurian @daniel\r\n- [ ] Sign up for sciserver account\r\n  http://www.sciserver.org/tools/compute/\r\n- [x] Tony will give you a numpy array representing a brain\r\n    - The numpy array is under /Tony/Fear199ds100ITKFile.npy\r\n- [ ] Using numpy, scikit, and matplotlib, construct as many statistical analyses of the brains that you can\r\n- [ ] Type up a latex report on findings\r\n"},"comment":{"url":"https://api.github.com/repos/NeuroDataDesign/seelviz/issues/comments/257460321","html_url":"https://github.com/NeuroDataDesign/seelviz/issues/26#issuecomment-257460321","issue_url":"https://api.github.com/repos/NeuroDataDesign/seelviz/issues/26","id":257460321,"user":{"login":"mnatenz1","id":19764149,"avatar_url":"https://avatars.githubusercontent.com/u/19764149?v=3","gravatar_id":"","url":"https://api.github.com/users/mnatenz1","html_url":"https://github.com/mnatenz1","followers_url":"https://api.github.com/users/mnatenz1/followers","following_url":"https://api.github.com/users/mnatenz1/following{/other_user}","gists_url":"https://api.github.com/users/mnatenz1/gists{/gist_id}","starred_url":"https://api.github.com/users/mnatenz1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mnatenz1/subscriptions","organizations_url":"https://api.github.com/users/mnatenz1/orgs","repos_url":"https://api.github.com/users/mnatenz1/repos","events_url":"https://api.github.com/users/mnatenz1/events{/privacy}","received_events_url":"https://api.github.com/users/mnatenz1/received_events","type":"User","site_admin":false},"created_at":"2016-11-01T00:27:36Z","updated_at":"2016-11-01T00:27:36Z","body":"@toekneesunshine It would be awesome if you could title the plots, label axes, and include a short comment under each plot describing what's being represented by the plot. Otherwise I feel like I'm spending too effort on trying to understand what the plot is trying to show me, rather than trying to understand what the significance of the plotted results is. "}}
{"actor":{"display_login":"mnatenz1"}}