Reading CZI series

Hi,

 

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

 

Thanks for any help,

Flo

Hi Flo,

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?

Thank you and sorry for the trouble,

Christian

 

Thank you for the response.

 

I’m happy to give you some example data.

 

First one contains a (96) Well experiment with 9 images per well position (czi file). So 96 Wells * 9 Images per Well position = 864 Images.

--> https://www.dropbox.com/s/qpymrp1sk65pszf/Well.zip

 

The second one contains a little more complicated experiments with Z stacks, more channels and time series.

--> https://www.dropbox.com/s/o5oxy4jlp5vsxm8/Experiments.zip

 

Hopefully the files will help you.

Thanks a lot,

Flo

 

ps.:

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.

Well the second problem is really weird.

I made a workflow for that. There are two exact same paths and Nodes. The one with a tif image loaded works perfect.

The second with czi image loaded works fine except of the Interactive Segmentation View.

 

--> https://www.dropbox.com/s/uqhz4peyczy9ys3/Hilite%20workflow%20tif%20-%20czi.zip

 

Thanks.

Flo

Hi Flo,

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!

Good morning Christian,

HiLiting works now. Thanks a lot :)

 

Flo

Hi Flo,

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.

Best,

Martin

Hi Martin,

 

I tried it out and it looks very good now :)

 

Thanks a lot for the great work.

 

Flo

Hi all,

 

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?

 

 

Hi Flo,

I think the transformation of labels doesn't work anymore, right?  This problem will be fixed next week.

Christian

Thats right. Ok thanks. Please tell me when it's done because I want to present KNIP in our firm.

Hi Flo,

should be fixed with tomorrows nightly build. let me know if it works and thanks for reporting!

Christian

PS: Welcome back :-)

Nightly build should be online! let me know if you encounter any problems...

 

cheers,

Christian

I've just tested it and it works fine again. :-)

Thanks a lot.

 

Flo

I've just tested it and it works fine again. :-)

Thanks a lot.

 

Flo

perfect. thanks for letting me know.