{"action":"created","issue":{"url":"https://api.github.com/repos/qupath/qupath/issues/141","repository_url":"https://api.github.com/repos/qupath/qupath","labels_url":"https://api.github.com/repos/qupath/qupath/issues/141/labels{/name}","comments_url":"https://api.github.com/repos/qupath/qupath/issues/141/comments","events_url":"https://api.github.com/repos/qupath/qupath/issues/141/events","html_url":"https://github.com/qupath/qupath/issues/141","id":289591355,"node_id":"MDU6SXNzdWUyODk1OTEzNTU=","number":141,"title":".SCN files not opening correctly","user":{"login":"MustafaElshani","id":35562636,"node_id":"MDQ6VXNlcjM1NTYyNjM2","avatar_url":"https://avatars1.githubusercontent.com/u/35562636?v=4","gravatar_id":"","url":"https://api.github.com/users/MustafaElshani","html_url":"https://github.com/MustafaElshani","followers_url":"https://api.github.com/users/MustafaElshani/followers","following_url":"https://api.github.com/users/MustafaElshani/following{/other_user}","gists_url":"https://api.github.com/users/MustafaElshani/gists{/gist_id}","starred_url":"https://api.github.com/users/MustafaElshani/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MustafaElshani/subscriptions","organizations_url":"https://api.github.com/users/MustafaElshani/orgs","repos_url":"https://api.github.com/users/MustafaElshani/repos","events_url":"https://api.github.com/users/MustafaElshani/events{/privacy}","received_events_url":"https://api.github.com/users/MustafaElshani/received_events","type":"User","site_admin":false},"labels":[{"id":721668629,"node_id":"MDU6TGFiZWw3MjE2Njg2Mjk=","url":"https://api.github.com/repos/qupath/qupath/labels/file%20formats","name":"file formats","color":"fbca04","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":12,"created_at":"2018-01-18T11:13:19Z","updated_at":"2018-06-25T17:01:47Z","closed_at":null,"author_association":"NONE","body":"Hi Guys \r\nWe are having trouble opening .SCN files, when we open an HE scan it does not display correctly with a Pink overlay. Also it seems that QuPath does not recognise it as HE but rather as fluorescence, I have tried to change to HE but with the same result. Have also tried to change the Brightness Contrast to no effect. The zoom feature does not seem to function even when viewing the actual slide image.\r\n\r\n![qupath scn error](https://user-images.githubusercontent.com/35562636/35095344-076ed048-fc40-11e7-8a1e-3ab26579946a.png)\r\n\r\nYour help would be very much appreciated \r\n\r\nKindest of Regards\r\n"},"comment":{"url":"https://api.github.com/repos/qupath/qupath/issues/comments/400023655","html_url":"https://github.com/qupath/qupath/issues/141#issuecomment-400023655","issue_url":"https://api.github.com/repos/qupath/qupath/issues/141","id":400023655,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMDAyMzY1NQ==","user":{"login":"BenjiP87","id":38423460,"node_id":"MDQ6VXNlcjM4NDIzNDYw","avatar_url":"https://avatars0.githubusercontent.com/u/38423460?v=4","gravatar_id":"","url":"https://api.github.com/users/BenjiP87","html_url":"https://github.com/BenjiP87","followers_url":"https://api.github.com/users/BenjiP87/followers","following_url":"https://api.github.com/users/BenjiP87/following{/other_user}","gists_url":"https://api.github.com/users/BenjiP87/gists{/gist_id}","starred_url":"https://api.github.com/users/BenjiP87/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BenjiP87/subscriptions","organizations_url":"https://api.github.com/users/BenjiP87/orgs","repos_url":"https://api.github.com/users/BenjiP87/repos","events_url":"https://api.github.com/users/BenjiP87/events{/privacy}","received_events_url":"https://api.github.com/users/BenjiP87/received_events","type":"User","site_admin":false},"created_at":"2018-06-25T17:01:47Z","updated_at":"2018-06-25T17:01:47Z","author_association":"NONE","body":"I also had some problems using the bioformats package and scn files.  After installing the plugin, when I try to open my images on qupath, qupath tries to open my scn files using the bioformats server (not openslide)  and it cannot determine the magnification metadata   I tried manually editing the metadata into the qpproj file, but this had no effect.  Turning off the bioformats plugin in edit>preferences resolved my error."}}
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