I tried to read CZI files with the Image Reader. The CZI file contains a series of images. On Additional Options -> Series & Groups when I click “Read all series”, I get only one (always the first of the series) image.
I also get the follow error message:
ERROR ReadFileImgTable java.lang.IllegalStateException: Image data for the file C:\Users\user\Desktop\Export_Test2\SW\96Well_1-Scene-01-A1-A1.czi has already been read and reader is closed!
ERROR ReadFileImgTable java.lang.IllegalStateException: Image data for the file C:\Users\user\Desktop\Export_Test2\SW\96Well_1-Scene-01-A1-A1.czi has already been read and reader is closed!
ERROR ReadFileImgTable java.lang.IllegalStateException: Image data for the file C:\Users\user\Desktop\Export_Test2\SW\96Well_1-Scene-01-A1-A1.czi has already been read and reader is closed!
ERROR ReadFileImgTable java.lang.IllegalStateException: Image data for the file C:\Users\user\Desktop\Export_Test2\SW\96Well_1-Scene-01-A1-A1.czi has already been read and reader is closed!
ERROR ReadFileImgTable java.lang.IllegalStateException: Image data for the file C:\Users\user\Desktop\Export_Test2\SW\96Well_1-Scene-01-A1-A1.czi has already been read and reader is closed!
ERROR ReadFileImgTable java.lang.IllegalStateException: Image data for the file C:\Users\user\Desktop\Export_Test2\SW\96Well_1-Scene-01-A1-A1.czi has already been read and reader is closed!
ERROR ReadFileImgTable java.lang.IllegalStateException: Image data for the file C:\Users\user\Desktop\Export_Test2\SW\96Well_1-Scene-01-A1-A1.czi has already been read and reader is closed!
ERROR ReadFileImgTable java.lang.IllegalStateException: Image data for the file C:\Users\user\Desktop\Export_Test2\SW\96Well_1-Scene-01-A1-A1.czi has already been read and reader is closed!
ERROR Image Reader Execute failed: Encountered duplicate row ID "C:\Users\user\Desktop\Export_Test2\SW\96Well_1-Scene-01-A1-A1.czi" at row number 3
But instead of using “Read all series” if I choose one image from the series by setting the “Series index” it works fine and I get the Image I have chosen
sorry for the delay with the response. Your problem is well known at it seems to be a problem with the bioformats library we use to read/write images. We will update our bioformats libraries these days and then we would like to try your files. Would it be possible to provide us some example data such that we can test with the new bioformats version and in the case it still doesn't work provide the data the maintainers of bioformats/scifio such that they can fix the bug?
An other problem had occurred with the czi file format.
We tried to use the (very useful) Hilite mode with the Interactive Segmentation View, the Interactive Table and the Scatter Plot Nodes.
With tif format it worked great. With czi files we Hilited points in the Scatter Plot and in the Interactive Table they appeared right but unfortunately in the Interactive Segmentation View the Hilited points didn’t show up (Hilite Mode was on).
Thank you Flo! We will have a look and try to fix the problems with czi.
Concerning the other problem: Actually, as soon as the image is read in, all the images have the same format (this means a special KNIME format), so the problem with the hiliting you described can't be related to the file-format. Anyway, again: If you upload a small example workflow here I will have a look and see what's going wrong :-)
Cheers,
Christian
PS: If you have any other feedback, suggestions, difficulties, please let us know! Such feedback is extremly helpful and we really want to improve KNIP.
I found the problem regarding the hiliting. The problem actually really is related to czi, but just as we try to read them in as a series. Here the problem (and solution):
The segment feature node extracts each and every segment and creates a table, one row for each segment. The RowIDs of these tables have to be unique, thats why we append #Label to the RowID. Usually the original RowID of the Labeling and the name of the Labeling are the same, but in the case of czi, the name is "File.czi" and the RowID is "File.czi_01". The "01" is as we read in a series of files and have to somehow unify the RowIDs. In the SegmentHilite node configuration, you use $LabelingName$#$Label$ as the format of the RowIDs of the input table. In the case of czi you should use $RowId$#$label$.
Of course this is not very intuitive and somehow confusing, but I promise that we really try hard to make the hiliting more transparent and easy in the future.
I hope this helps!
Christian
PS: Martin is working on your problem with reading czi and it seems that we also have a solution for this issue pretty soon!
the problem to read czi-files should be fixed now and is available via the nightly-build update site of the plugin (see instructions how to get the nightly builds). If you don't want to switch to the nighlty build than the change will be available with the next bugfix-release, presumably to be released in a couple of days.
after updating KNIME 2 to version 3 (3.1.1) the Hilite feature in the Interactive Segmentation View doesn't work anymore. In the Interactive Table or Scatter Plot it seems to work just fine. Or is there something I have to change in the options after updating?