{"action":"created","issue":{"url":"https://api.github.com/repos/cortex-lab/Suite2P/issues/152","repository_url":"https://api.github.com/repos/cortex-lab/Suite2P","labels_url":"https://api.github.com/repos/cortex-lab/Suite2P/issues/152/labels{/name}","comments_url":"https://api.github.com/repos/cortex-lab/Suite2P/issues/152/comments","events_url":"https://api.github.com/repos/cortex-lab/Suite2P/issues/152/events","html_url":"https://github.com/cortex-lab/Suite2P/issues/152","id":370863977,"node_id":"MDU6SXNzdWUzNzA4NjM5Nzc=","number":152,"title":"Data Format Questions on Image Registration","user":{"login":"danachang","id":11020948,"node_id":"MDQ6VXNlcjExMDIwOTQ4","avatar_url":"https://avatars1.githubusercontent.com/u/11020948?v=4","gravatar_id":"","url":"https://api.github.com/users/danachang","html_url":"https://github.com/danachang","followers_url":"https://api.github.com/users/danachang/followers","following_url":"https://api.github.com/users/danachang/following{/other_user}","gists_url":"https://api.github.com/users/danachang/gists{/gist_id}","starred_url":"https://api.github.com/users/danachang/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/danachang/subscriptions","organizations_url":"https://api.github.com/users/danachang/orgs","repos_url":"https://api.github.com/users/danachang/repos","events_url":"https://api.github.com/users/danachang/events{/privacy}","received_events_url":"https://api.github.com/users/danachang/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2018-10-17T01:42:07Z","updated_at":"2018-10-17T18:41:00Z","closed_at":null,"author_association":"NONE","body":"Hi, I am still confused at data format required for image registration after reading the README and glance through the scripts. \r\n\r\nMy 2P data is acquired with red (Ch1) and green (Ch2) channels using the Bruker system.  Each plane is stored in one unique folder, where each frame is also saved as one TIFF file. Ch1 and Ch2 are also saved separately. For example, for one single plane, I would have files saved like this:\r\n```\r\nxxx_Ch1_0001.tif  \r\nxxx_Ch1_0002.tif  \r\nxxx_Ch2_0001.tif  \r\nxxx_Ch2_0002.tif\r\n```\r\nDoes Suie2P assume all the frames/channels are saved in one single TIFF? Does Suite2P support this kind of file format? If yes, should I just go ahead and set `ops.nchannels = 2`, `ops.rchannel = 1`, `ops.gchannel = 2`, and `ops.AlignToRedChannel = 1`? \r\n\r\nThanks,\r\ndana"},"comment":{"url":"https://api.github.com/repos/cortex-lab/Suite2P/issues/comments/430742399","html_url":"https://github.com/cortex-lab/Suite2P/issues/152#issuecomment-430742399","issue_url":"https://api.github.com/repos/cortex-lab/Suite2P/issues/152","id":430742399,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMDc0MjM5OQ==","user":{"login":"carsen-stringer","id":15067541,"node_id":"MDQ6VXNlcjE1MDY3NTQx","avatar_url":"https://avatars3.githubusercontent.com/u/15067541?v=4","gravatar_id":"","url":"https://api.github.com/users/carsen-stringer","html_url":"https://github.com/carsen-stringer","followers_url":"https://api.github.com/users/carsen-stringer/followers","following_url":"https://api.github.com/users/carsen-stringer/following{/other_user}","gists_url":"https://api.github.com/users/carsen-stringer/gists{/gist_id}","starred_url":"https://api.github.com/users/carsen-stringer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/carsen-stringer/subscriptions","organizations_url":"https://api.github.com/users/carsen-stringer/orgs","repos_url":"https://api.github.com/users/carsen-stringer/repos","events_url":"https://api.github.com/users/carsen-stringer/events{/privacy}","received_events_url":"https://api.github.com/users/carsen-stringer/received_events","type":"User","site_admin":false},"created_at":"2018-10-17T18:41:00Z","updated_at":"2018-10-17T18:41:00Z","author_association":"COLLABORATOR","body":"Sorry there isn't good documentation on this. The pipeline allows you to have separate folders with different numbers of channels (say you don't collect the red channel during the whole experiment). That's when you would have `expts` not equal `expred`. `nchannels` refers to the number of channels in `expts` and `nchannels_red` refers to the number of channels in `expred`. In your case you should say\r\n`\r\ndb(i).expts = 1;\r\ndb(i).nchannels = 2;\r\ndb(i).expred = db(i).expred;\r\ndb(i).nchannels_red  = db(i).nchannels;\r\n`\r\nAlso, if you're comfortable with python, I'd recommend using that pipeline, we've made some upgrades to that one, and the GUI is much better. You can run the pipeline from the GUI and this part is less confusing because we don't allow different blocks of the experiment with different channel numbers :)"}}
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