{"action":"created","issue":{"url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2558","repository_url":"https://api.github.com/repos/openmicroscopy/bioformats","labels_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2558/labels{/name}","comments_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2558/comments","events_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2558/events","html_url":"https://github.com/openmicroscopy/bioformats/issues/2558","id":174935560,"number":2558,"title":"Problem with Reading Image Series Dimension with BioFormats 5.2.1","user":{"login":"sebi06","id":3833249,"avatar_url":"https://avatars.githubusercontent.com/u/3833249?v=3","gravatar_id":"","url":"https://api.github.com/users/sebi06","html_url":"https://github.com/sebi06","followers_url":"https://api.github.com/users/sebi06/followers","following_url":"https://api.github.com/users/sebi06/following{/other_user}","gists_url":"https://api.github.com/users/sebi06/gists{/gist_id}","starred_url":"https://api.github.com/users/sebi06/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sebi06/subscriptions","organizations_url":"https://api.github.com/users/sebi06/orgs","repos_url":"https://api.github.com/users/sebi06/repos","events_url":"https://api.github.com/users/sebi06/events{/privacy}","received_events_url":"https://api.github.com/users/sebi06/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-09-04T07:18:11Z","updated_at":"2016-09-06T10:12:40Z","closed_at":null,"body":"Hi Guys,\r\n\r\ni test one of my testfiles yesterday with the BioFormats 5.2.1 and ran into an issue I do not understand yet. The file is a 3x3 tile image with 10% overlap and just one channel, where a frame is 640x640. Wirh former bioformtas this resulted always in 9 image series (one for each tile) with 640x640.\r\nNow I wanted to check out the new features, where my expectation is that it results in only one image series with 1792 x 1792 size.\r\n\r\nBut with BioFormats 5.2.1 and my testscripts now give me 2 image series, which does not really makes sense to me. Is this a bug or am I missing somethig?\r\nWith 5.1.10 everything works normal and I get only one image series\r\n\r\nTestfile: https://dl.dropboxusercontent.com/u/623476/3x3Tile_CH%3D1.czi\r\n\r\nHelp i really appreciated,\r\nSebi\r\n\r\nHere is the output for the testfile using BF 5.1.10 vs. 5.2.1.\r\n\r\n[3x3Tile_CH=1_BF5.1.10_output.txt](https://github.com/openmicroscopy/bioformats/files/453818/3x3Tile_CH.1_BF5.1.10_output.txt)\r\n[3x3Tile_CH=1_BF5.2.1_output.txt](https://github.com/openmicroscopy/bioformats/files/453819/3x3Tile_CH.1_BF5.2.1_output.txt)\r\n"},"comment":{"url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/comments/244908074","html_url":"https://github.com/openmicroscopy/bioformats/issues/2558#issuecomment-244908074","issue_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2558","id":244908074,"user":{"login":"sbesson","id":1355463,"avatar_url":"https://avatars.githubusercontent.com/u/1355463?v=3","gravatar_id":"","url":"https://api.github.com/users/sbesson","html_url":"https://github.com/sbesson","followers_url":"https://api.github.com/users/sbesson/followers","following_url":"https://api.github.com/users/sbesson/following{/other_user}","gists_url":"https://api.github.com/users/sbesson/gists{/gist_id}","starred_url":"https://api.github.com/users/sbesson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sbesson/subscriptions","organizations_url":"https://api.github.com/users/sbesson/orgs","repos_url":"https://api.github.com/users/sbesson/repos","events_url":"https://api.github.com/users/sbesson/events{/privacy}","received_events_url":"https://api.github.com/users/sbesson/received_events","type":"User","site_admin":false},"created_at":"2016-09-06T10:12:40Z","updated_at":"2016-09-06T10:12:40Z","body":"@sebi06: so using your example file, the behavior depends on whether subresolutions are flattened as series or not. In the former case, 8 series will be detected (one for each scene and resolution):\r\n\r\n```\r\n$ showinf -nopix -nometa Pos\\=2_3x3_Tile+9x9Tile_CH\\=1.czi \r\nChecking file format [Zeiss CZI]\r\nInitializing reader\r\nZeissCZIReader initializing Pos=2_3x3_Tile+9x9Tile_CH=1.czi\r\nInitialization took 0.377s\r\n\r\nReading core metadata\r\nfilename = Pos=2_3x3_Tile+9x9Tile_CH=1.czi\r\nSeries count = 8\r\nSeries #0 :\r\n\tImage count = 1\r\n\tRGB = false (1) \r\n\tInterleaved = false\r\n\tIndexed = false (false color)\r\n\tWidth = 1792\r\n\tHeight = 1792\r\n\tSizeZ = 1\r\n\tSizeT = 1\r\n\tSizeC = 1\r\n\tThumbnail size = 128 x 128\r\n\tEndianness = intel (little)\r\n\tDimension order = XYCZT (certain)\r\n\tPixel type = uint8\r\n\tValid bits per pixel = 8\r\n\tMetadata complete = false\r\n\tThumbnail series = false\r\nSeries #1 :\r\n\tImage count = 1\r\n\tRGB = false (1) \r\n\tInterleaved = false\r\n\tIndexed = false (false color)\r\n\tWidth = 896\r\n\tHeight = 896\r\n\tSizeZ = 1\r\n\tSizeT = 1\r\n\tSizeC = 1\r\n\tThumbnail size = 128 x 128\r\n\tEndianness = intel (little)\r\n\tDimension order = XYCZT (certain)\r\n\tPixel type = uint8\r\n\tValid bits per pixel = 8\r\n\tMetadata complete = false\r\n\tThumbnail series = false\r\nSeries #2 :\r\n\tImage count = 1\r\n\tRGB = false (1) \r\n\tInterleaved = false\r\n\tIndexed = false (false color)\r\n\tWidth = 448\r\n\tHeight = 448\r\n\tSizeZ = 1\r\n\tSizeT = 1\r\n\tSizeC = 1\r\n\tThumbnail size = 128 x 128\r\n\tEndianness = intel (little)\r\n\tDimension order = XYCZT (certain)\r\n\tPixel type = uint8\r\n\tValid bits per pixel = 8\r\n\tMetadata complete = false\r\n\tThumbnail series = false\r\nSeries #3 :\r\n\tImage count = 1\r\n\tRGB = false (1) \r\n\tInterleaved = false\r\n\tIndexed = false (false color)\r\n\tWidth = 224\r\n\tHeight = 224\r\n\tSizeZ = 1\r\n\tSizeT = 1\r\n\tSizeC = 1\r\n\tThumbnail size = 128 x 128\r\n\tEndianness = intel (little)\r\n\tDimension order = XYCZT (certain)\r\n\tPixel type = uint8\r\n\tValid bits per pixel = 8\r\n\tMetadata complete = false\r\n\tThumbnail series = false\r\nSeries #4 :\r\n\tImage count = 1\r\n\tRGB = false (1) \r\n\tInterleaved = false\r\n\tIndexed = false (false color)\r\n\tWidth = 5248\r\n\tHeight = 5248\r\n\tSizeZ = 1\r\n\tSizeT = 1\r\n\tSizeC = 1\r\n\tThumbnail size = 128 x 128\r\n\tEndianness = intel (little)\r\n\tDimension order = XYCZT (certain)\r\n\tPixel type = uint8\r\n\tValid bits per pixel = 8\r\n\tMetadata complete = false\r\n\tThumbnail series = false\r\nSeries #5 :\r\n\tImage count = 1\r\n\tRGB = false (1) \r\n\tInterleaved = false\r\n\tIndexed = false (false color)\r\n\tWidth = 2624\r\n\tHeight = 2624\r\n\tSizeZ = 1\r\n\tSizeT = 1\r\n\tSizeC = 1\r\n\tThumbnail size = 128 x 128\r\n\tEndianness = intel (little)\r\n\tDimension order = XYCZT (certain)\r\n\tPixel type = uint8\r\n\tValid bits per pixel = 8\r\n\tMetadata complete = false\r\n\tThumbnail series = false\r\nSeries #6 :\r\n\tImage count = 1\r\n\tRGB = false (1) \r\n\tInterleaved = false\r\n\tIndexed = false (false color)\r\n\tWidth = 1312\r\n\tHeight = 1312\r\n\tSizeZ = 1\r\n\tSizeT = 1\r\n\tSizeC = 1\r\n\tThumbnail size = 128 x 128\r\n\tEndianness = intel (little)\r\n\tDimension order = XYCZT (certain)\r\n\tPixel type = uint8\r\n\tValid bits per pixel = 8\r\n\tMetadata complete = false\r\n\tThumbnail series = false\r\nSeries #7 :\r\n\tImage count = 1\r\n\tRGB = false (1) \r\n\tInterleaved = false\r\n\tIndexed = false (false color)\r\n\tWidth = 656\r\n\tHeight = 656\r\n\tSizeZ = 1\r\n\tSizeT = 1\r\n\tSizeC = 1\r\n\tThumbnail size = 128 x 128\r\n\tEndianness = intel (little)\r\n\tDimension order = XYCZT (certain)\r\n\tPixel type = uint8\r\n\tValid bits per pixel = 8\r\n\tMetadata complete = false\r\n\tThumbnail series = false\r\n```\r\n\r\nIf resolutions are not flattened then 2 series will be detected (one per scene) containing 4 levels of resolution each.\r\n\r\n```\r\n$ showinf -nopix -nometa -noflat Pos\\=2_3x3_Tile+9x9Tile_CH\\=1.czi \r\nChecking file format [Zeiss CZI]\r\nInitializing reader\r\nZeissCZIReader initializing Pos=2_3x3_Tile+9x9Tile_CH=1.czi\r\nInitialization took 0.35s\r\n\r\nReading core metadata\r\nfilename = Pos=2_3x3_Tile+9x9Tile_CH=1.czi\r\nSeries count = 2\r\nSeries #0 :\r\n\tResolutions = 4\r\n\t\tsizeX[0] = 1792\r\n\t\tsizeX[1] = 896\r\n\t\tsizeX[2] = 448\r\n\t\tsizeX[3] = 224\r\n\tImage count = 1\r\n\tRGB = false (1) \r\n\tInterleaved = false\r\n\tIndexed = false (false color)\r\n\tWidth = 1792\r\n\tHeight = 1792\r\n\tSizeZ = 1\r\n\tSizeT = 1\r\n\tSizeC = 1\r\n\tThumbnail size = 128 x 128\r\n\tEndianness = intel (little)\r\n\tDimension order = XYCZT (certain)\r\n\tPixel type = uint8\r\n\tValid bits per pixel = 8\r\n\tMetadata complete = false\r\n\tThumbnail series = false\r\nSeries #1 :\r\n\tResolutions = 4\r\n\t\tsizeX[0] = 5248\r\n\t\tsizeX[1] = 2624\r\n\t\tsizeX[2] = 1312\r\n\t\tsizeX[3] = 656\r\n\tImage count = 1\r\n\tRGB = false (1) \r\n\tInterleaved = false\r\n\tIndexed = false (false color)\r\n\tWidth = 5248\r\n\tHeight = 5248\r\n\tSizeZ = 1\r\n\tSizeT = 1\r\n\tSizeC = 1\r\n\tThumbnail size = 128 x 128\r\n\tEndianness = intel (little)\r\n\tDimension order = XYCZT (certain)\r\n\tPixel type = uint8\r\n\tValid bits per pixel = 8\r\n\tMetadata complete = false\r\n\tThumbnail series = false\r\n```\r\n\r\nOn the python-bioformats front, looking at the code, it looks like every method needs to be exposed via the Java bridge. Opening an issue on their repository to discuss the API addition might be a starting point as I do not know about theor roadmap."}}
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