{"action":"created","issue":{"url":"https://api.github.com/repos/losonczylab/sima/issues/195","labels_url":"https://api.github.com/repos/losonczylab/sima/issues/195/labels{/name}","comments_url":"https://api.github.com/repos/losonczylab/sima/issues/195/comments","events_url":"https://api.github.com/repos/losonczylab/sima/issues/195/events","html_url":"https://github.com/losonczylab/sima/issues/195","id":105117298,"number":195,"title":"\"Failed to estimate positive gains\"","user":{"login":"vjlbym","id":11791828,"avatar_url":"https://avatars.githubusercontent.com/u/11791828?v=3","gravatar_id":"","url":"https://api.github.com/users/vjlbym","html_url":"https://github.com/vjlbym","followers_url":"https://api.github.com/users/vjlbym/followers","following_url":"https://api.github.com/users/vjlbym/following{/other_user}","gists_url":"https://api.github.com/users/vjlbym/gists{/gist_id}","starred_url":"https://api.github.com/users/vjlbym/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vjlbym/subscriptions","organizations_url":"https://api.github.com/users/vjlbym/orgs","repos_url":"https://api.github.com/users/vjlbym/repos","events_url":"https://api.github.com/users/vjlbym/events{/privacy}","received_events_url":"https://api.github.com/users/vjlbym/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-09-06T21:14:14Z","updated_at":"2015-09-09T20:36:53Z","closed_at":null,"body":"Hi,\r\n\r\nI've been trying to get SIMA to run motion correction on a 5 gb video acquired with a 2P microscope using resonant scanning at 2.5 Hz for 2 hours. I am running it on a really beefed up computer on Amazon EC2, which has about 64 gb of RAM. I've been getting an error saying \"Failed to estimate positive gains\". I understand that this is a step involving the calculation of expected photon count to pixel intensity. I've not gotten such an error on many other files that I've run, all of which are considerably smaller than this file. Could you guys please let me know what the issue is? Does it have to do with the file size?\r\n\r\nAlso, is the motion correction tuned to work better for galvo scan compared to resonant scans on a 2P scope?\r\n\r\nThanks a lot!\r\nVijay"},"comment":{"url":"https://api.github.com/repos/losonczylab/sima/issues/comments/139038481","html_url":"https://github.com/losonczylab/sima/issues/195#issuecomment-139038481","issue_url":"https://api.github.com/repos/losonczylab/sima/issues/195","id":139038481,"user":{"login":"vjlbym","id":11791828,"avatar_url":"https://avatars.githubusercontent.com/u/11791828?v=3","gravatar_id":"","url":"https://api.github.com/users/vjlbym","html_url":"https://github.com/vjlbym","followers_url":"https://api.github.com/users/vjlbym/followers","following_url":"https://api.github.com/users/vjlbym/following{/other_user}","gists_url":"https://api.github.com/users/vjlbym/gists{/gist_id}","starred_url":"https://api.github.com/users/vjlbym/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vjlbym/subscriptions","organizations_url":"https://api.github.com/users/vjlbym/orgs","repos_url":"https://api.github.com/users/vjlbym/repos","events_url":"https://api.github.com/users/vjlbym/events{/privacy}","received_events_url":"https://api.github.com/users/vjlbym/received_events","type":"User","site_admin":false},"created_at":"2015-09-09T20:36:53Z","updated_at":"2015-09-09T20:36:53Z","body":"I just figured out that the issue is that the data did not load correctly. I haven't yet figured out what the issue is, though.\r\nI used `sequences = sima.sequences.create(`TIFF`,<path>)` and it treated this tiff stack as a single image tiff file, or at least, loaded in only one frame. ImageJ loads it in fine. I've tried two files, one that is 5 gb and another that is 12gb and they both fail to import more than one frame.\r\n\r\nOne thing to note is that this file was concatenated in imagej from individual tiff stacks. I can load in each of those tiff stacks without any problem. But when I load the concatenated ones, even though imageJ stores it as a tif stack, SIMA fails to import more than one frame.\r\n\r\nAny clues what might be up?\r\n\r\nThanks!"}}