{"action":"created","issue":{"url":"https://api.github.com/repos/dpschreiner/icb/issues/15","repository_url":"https://api.github.com/repos/dpschreiner/icb","labels_url":"https://api.github.com/repos/dpschreiner/icb/issues/15/labels{/name}","comments_url":"https://api.github.com/repos/dpschreiner/icb/issues/15/comments","events_url":"https://api.github.com/repos/dpschreiner/icb/issues/15/events","html_url":"https://github.com/dpschreiner/icb/issues/15","id":171049644,"number":15,"title":"Pipeline flow details","user":{"login":"dpschreiner","id":4560485,"avatar_url":"https://avatars.githubusercontent.com/u/4560485?v=3","gravatar_id":"","url":"https://api.github.com/users/dpschreiner","html_url":"https://github.com/dpschreiner","followers_url":"https://api.github.com/users/dpschreiner/followers","following_url":"https://api.github.com/users/dpschreiner/following{/other_user}","gists_url":"https://api.github.com/users/dpschreiner/gists{/gist_id}","starred_url":"https://api.github.com/users/dpschreiner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpschreiner/subscriptions","organizations_url":"https://api.github.com/users/dpschreiner/orgs","repos_url":"https://api.github.com/users/dpschreiner/repos","events_url":"https://api.github.com/users/dpschreiner/events{/privacy}","received_events_url":"https://api.github.com/users/dpschreiner/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/dpschreiner/icb/labels/metadata","name":"metadata","color":"5319e7"},{"url":"https://api.github.com/repos/dpschreiner/icb/labels/pipeline","name":"pipeline","color":"c5def5"}],"state":"open","locked":false,"assignee":{"login":"dpschreiner","id":4560485,"avatar_url":"https://avatars.githubusercontent.com/u/4560485?v=3","gravatar_id":"","url":"https://api.github.com/users/dpschreiner","html_url":"https://github.com/dpschreiner","followers_url":"https://api.github.com/users/dpschreiner/followers","following_url":"https://api.github.com/users/dpschreiner/following{/other_user}","gists_url":"https://api.github.com/users/dpschreiner/gists{/gist_id}","starred_url":"https://api.github.com/users/dpschreiner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpschreiner/subscriptions","organizations_url":"https://api.github.com/users/dpschreiner/orgs","repos_url":"https://api.github.com/users/dpschreiner/repos","events_url":"https://api.github.com/users/dpschreiner/events{/privacy}","received_events_url":"https://api.github.com/users/dpschreiner/received_events","type":"User","site_admin":false},"assignees":[{"login":"dpschreiner","id":4560485,"avatar_url":"https://avatars.githubusercontent.com/u/4560485?v=3","gravatar_id":"","url":"https://api.github.com/users/dpschreiner","html_url":"https://github.com/dpschreiner","followers_url":"https://api.github.com/users/dpschreiner/followers","following_url":"https://api.github.com/users/dpschreiner/following{/other_user}","gists_url":"https://api.github.com/users/dpschreiner/gists{/gist_id}","starred_url":"https://api.github.com/users/dpschreiner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpschreiner/subscriptions","organizations_url":"https://api.github.com/users/dpschreiner/orgs","repos_url":"https://api.github.com/users/dpschreiner/repos","events_url":"https://api.github.com/users/dpschreiner/events{/privacy}","received_events_url":"https://api.github.com/users/dpschreiner/received_events","type":"User","site_admin":false}],"milestone":null,"comments":0,"created_at":"2016-08-14T09:05:50Z","updated_at":"2016-09-23T08:33:40Z","closed_at":null,"body":"## Tentative Automated Pipeline Flow\r\n\r\n1. **acquisition** (PNG [conversion] or TIFF [no conversion]) #7, #8 onto external Thunderbox RAID\r\n1. create **project in DB** (e.g. Omero), e.g. \"CD62L 2016-07-20\"\r\n1. create **datasets within project** in DB, e.g. \"CD62L High\", \"CD62L Low 2/2\"\r\n1. bring Thunderbox to lab, connect to our machine\r\n1. [option 1 - convert to 8 bit **on our machine** before import]\r\n 1. calculate **extrema** (max/min) per wavelength (N.B. outliers: #14) **locally**\r\n 1. **convert to 8 bit** on our machine before import/upload\r\n1. create **OME-TIFF** on our machine (gensparse script #1, #4)\r\n1. **import filesets into Omero** - one per position, i.e. one movie, multiple wavelengths\r\n1. [option 2 - convert to 8 bit after import]\r\n 1. calculate **extrema** (max/min) per wavelength (N.B. outliers: #14) **on cluster**\r\n 1. **convert to 8 bit** -- separate CP pipeline headless or own script on cluster\r\n1. **store extrema metadata in project DB**\r\n1. **CP Illumination Correction** pipeline\r\n1. **TRACKING**\r\n 1. **TTT on local machine**\r\n 1. **CP TrackObjects** pipeline - manual testing to check thresholds etc\r\n1. Manual intervention for **correction of automatic tracking** - e.g. Traxtile #16\r\n1. **Quantification** of intensities (done by TrackObjects to some extent)\r\n1. **Statistical analysis**\r\n1. **Figures**\r\n\r\n- [ ] do it\r\n- [ ] to the other"},"comment":{"url":"https://api.github.com/repos/dpschreiner/icb/issues/comments/249134333","html_url":"https://github.com/dpschreiner/icb/issues/15#issuecomment-249134333","issue_url":"https://api.github.com/repos/dpschreiner/icb/issues/15","id":249134333,"user":{"login":"dpschreiner","id":4560485,"avatar_url":"https://avatars.githubusercontent.com/u/4560485?v=3","gravatar_id":"","url":"https://api.github.com/users/dpschreiner","html_url":"https://github.com/dpschreiner","followers_url":"https://api.github.com/users/dpschreiner/followers","following_url":"https://api.github.com/users/dpschreiner/following{/other_user}","gists_url":"https://api.github.com/users/dpschreiner/gists{/gist_id}","starred_url":"https://api.github.com/users/dpschreiner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpschreiner/subscriptions","organizations_url":"https://api.github.com/users/dpschreiner/orgs","repos_url":"https://api.github.com/users/dpschreiner/repos","events_url":"https://api.github.com/users/dpschreiner/events{/privacy}","received_events_url":"https://api.github.com/users/dpschreiner/received_events","type":"User","site_admin":false},"created_at":"2016-09-23T08:33:40Z","updated_at":"2016-09-23T08:33:40Z","body":"[short-term TTT-based](https://docs.google.com/drawings/d/18yUcbckY6GpeWGSJRnV691xWMBVbPYgIti92PyF0PGo/edit)\r\n\r\n[long-term CP-sciCORE-based](https://docs.google.com/drawings/d/1DSNRltCKGJS3AM8HCM07gUtBBQehFHmWSDf3A2mFOuk/edit)"}}
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