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

ilastik

#1

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 ?

Thnx.


#2

Hi @Eric.lindberg82.

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

Cheers


#3

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


#4

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)?


#5

No, it is generated in Ilastik


#6

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


#7

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


#8

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


#9

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?


#10

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


#11

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


#12

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


#13

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


#14

Those lines are generated by Ilastik, not drawn by me


#15

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


#16

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