Getting rid of the prediction lines in the probability maps after pixel classification



This might be a stupid question but, I was wondering about the prediction lines that pop up during segmentation during the pixel classification. When I export the probability maps I can see the lines when I display it in Fiji and Imaris. Is there and way to prevent this ?



Hi @Eric.lindberg82.

would it be possible for you to please post a screenshot of what you mean by prediction lines?



Thnx for your reply, please see attached file. I don’t understand why the lines are present in the final probability map file.


Oh. I don’t think I have ever seen something like this.

Is that pattern actually in your image data somewhere (maybe in a separate channel)?


No, it is generated in Ilastik


Would it be possible that you share an example dataset, ilastik project and output with us somehow and send a link to ?


Thank you for your reply, Im afraid I am not allowed to share any data directly due to institute policy.


These prediction lines somehow end up in the final probability map.
This happened in version 1.3 and also 1.3.2


I’m afraid that it will be really hard to help in your case. Those lines are no build-in feature of ilastik. It is either a bug, or something like this is somehow already in your data. If your data is multi-channel, have you looked at all channels independently?


Its not in the raw data trust me, it appears in Ilastik


Are you trying to segment via Weka?
If so it may be much better to just use the normal Threshold in Image.


@Eric.lindberg82, what are the red and cyan lines visible in the second image you have posted? Are those your annotations?


it will be very very hard to help you. really.


Those lines are generated by Ilastik, not drawn by me


Yes I know, but I cannot upload any data due to government regulations


I am segmenting by Ilastik, not the Weka imageJ plugin.