{"action":"created","issue":{"url":"https://api.github.com/repos/CovertLab/DeepCell/issues/13","repository_url":"https://api.github.com/repos/CovertLab/DeepCell","labels_url":"https://api.github.com/repos/CovertLab/DeepCell/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/CovertLab/DeepCell/issues/13/comments","events_url":"https://api.github.com/repos/CovertLab/DeepCell/issues/13/events","html_url":"https://github.com/CovertLab/DeepCell/issues/13","id":261950329,"number":13,"title":"Error when checking input: expected conv2d_1_input to have shape (None, 61, 61, 2)","user":{"login":"Vertislav","id":12300603,"avatar_url":"https://avatars3.githubusercontent.com/u/12300603?v=4","gravatar_id":"","url":"https://api.github.com/users/Vertislav","html_url":"https://github.com/Vertislav","followers_url":"https://api.github.com/users/Vertislav/followers","following_url":"https://api.github.com/users/Vertislav/following{/other_user}","gists_url":"https://api.github.com/users/Vertislav/gists{/gist_id}","starred_url":"https://api.github.com/users/Vertislav/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Vertislav/subscriptions","organizations_url":"https://api.github.com/users/Vertislav/orgs","repos_url":"https://api.github.com/users/Vertislav/repos","events_url":"https://api.github.com/users/Vertislav/events{/privacy}","received_events_url":"https://api.github.com/users/Vertislav/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2017-10-01T22:05:04Z","updated_at":"2017-10-03T19:50:06Z","closed_at":"2017-10-03T19:50:06Z","author_association":"NONE","body":"Good evening,\r\n\r\nIn last days I have found your article about DeepCell and it is very interesting and useful, thus I wish to apply it in future in my research. Currently I am trying to get into it with data provided by you, however, I have a problem with training the cov-net. I constantly get an error:\r\n\r\n> Error when checking input: expected conv2d_22_input to have shape (None, 61, 61, 2) but got array with shape (58859, 2, 61, 61)\r\n\r\nAs far as I understood (probably), script expects to have a TensorFlow format (NWHC, N-samples, width, height, class), but gets Theano format (NCWH). Is this a correct conclusion? Because I am using your npz files, I didn't modify them at all, python files as well, I am clueless what to do. \r\n\r\nI used **\"bn_feature_net_61x61\"** model on **3T3_all_61x61.npz** file (**Python 2.7, Ubuntu 16.04.3**). Previously I was trying _E. coli_ data as I am working with these organisms, but with 3T3 I progressed most.\r\n\r\nI am hoping for your answer and advise.\r\n\r\nKindly regards,\r\nBartosz"},"comment":{"url":"https://api.github.com/repos/CovertLab/DeepCell/issues/comments/333957739","html_url":"https://github.com/CovertLab/DeepCell/issues/13#issuecomment-333957739","issue_url":"https://api.github.com/repos/CovertLab/DeepCell/issues/13","id":333957739,"user":{"login":"Vertislav","id":12300603,"avatar_url":"https://avatars3.githubusercontent.com/u/12300603?v=4","gravatar_id":"","url":"https://api.github.com/users/Vertislav","html_url":"https://github.com/Vertislav","followers_url":"https://api.github.com/users/Vertislav/followers","following_url":"https://api.github.com/users/Vertislav/following{/other_user}","gists_url":"https://api.github.com/users/Vertislav/gists{/gist_id}","starred_url":"https://api.github.com/users/Vertislav/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Vertislav/subscriptions","organizations_url":"https://api.github.com/users/Vertislav/orgs","repos_url":"https://api.github.com/users/Vertislav/repos","events_url":"https://api.github.com/users/Vertislav/events{/privacy}","received_events_url":"https://api.github.com/users/Vertislav/received_events","type":"User","site_admin":false},"created_at":"2017-10-03T19:50:06Z","updated_at":"2017-10-03T19:50:06Z","author_association":"NONE","body":"Ok, problem is solved. I figured out that my keras was using TensorFlow backend and it should use Theano. Also, I reinstalled keras to older version. Both, E. coli and 3T3 cells are processed normally!\r\n\r\nThanks again for this fascinating approach in cell segmentation!\r\n\r\nBest,\r\nBartosz"}}
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