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Issue using Ilastik in Knime

Member for

1 year 11 months romainGuiet

Dear KNIME community,

While I managed to make a working workflow using Ilastik through KNIME on a 1 channel fluorescent dataset, I encounter some trouble on a dataset of RGB images.

The Ilastik project works fine on is own, but I have trouble once doing the integration in KNIME.
I wonder if Ilastik stand-alone (ISA) and Ilastik within KNIME (IWK) are reading the images in a different way.
I tried to convert RGB images to composite, some errors are gone but still IWK produce the error :
```
ERROR KNIPLogService                    File "C:\ilastik\ilastik-meta\lazyf=
low\lazyflow\operators\ioOperators\opTiffReader.py", line 88, in setupOutpu= ts
ERROR KNIPLogService                      assert P =3D=3D 1, "Don't know ho=
w to handle any number of planar samples per pixel except 1 (per page)"
ERROR KNIPLogService                  AssertionError: Don't know how to han=
dle any number of planar samples per pixel except 1 (per page) ERROR KNIPLogService
ERROR KNIPLogService                  ilastik error:
ERROR KNIPLogService                  The operation completed successfully.
```

Using this link you could download the projects, and the RGB and Composite = version of the images https://drive.switch.ch/index.php/s/uHraJwnCmFhzPTS

I'm looking forward to your answer,

Best regards,

Romain
 

Comments
Sat, 11/04/2017 - 10:19

Member for

6 years 6 months

gab1one

Hi Romain,

We just pushed a new version of our ilastik integration to the KNIP nightly build. I will look at your issues in more depth on Monday and report my findings.

best,

Gabriel

Mon, 12/04/2017 - 10:48

Member for

1 year 11 months

romainGuiet

Hi Gabriel,

I downloaded the last version but still couldn't make it work.

Did you have more succes than me ? 

Best,

Romain

 

Tue, 12/05/2017 - 05:37

Member for

6 years 6 months

gab1one

Hi Romain,

I am sorry you are still having trouble with Ilastik. I will look into it a bit more the next few days.

best,

Gabriel

Thu, 01/18/2018 - 02:48

Member for

1 year 11 months

romainGuiet

Hi Gabriel,

Wish you, and the team, all the best for 2018 ! 

Did you manage to make any progress on this topic ? 

Thanks again for your efforts,

Cheers,

Romain

 

Wed, 01/24/2018 - 12:05

Member for

6 years 6 months

gab1one

Hi Romain,

I am sorry to inform you that we did not manage to make any good progress on improving the Ilastik integration. I hope I can work on it in the next months.

best,

Gabriel