Problems importing labels

Hi @k-dominik,

My name is Lucía and I´m a new user of ilastik. I think it is really powerful but I´m having problems to share trained projects!! I ´m working in a microscopy facilty and try to help people to analyze their images that´s why I train the program to share the trained projects.

I trained a project in the Pixel Clasification mode, and when I felt It was working Ok, I tried to shared it with the people…and then I started to have problems.

I saw some tutorials but maybe I skiped the part when they said that you have to keep the training images in the same folder before start training. So I have a project that works nicely but I cannot change the path of the input images because is already trained.

What I did to try to overcome the problem was export de labels in .hdf5 and created a new project with the same training images and load the previosly exported labels for each image. It seemed to work fine, but i got two errors:

The first one, when I try to export the segmented image:

“Type error: sip.wrappertype object argumente after * must be an iterable, not int”

But it exported the images ok, even I could get the batched export images.
But when I tried to save this new project I got another error:

Error attemting Save:
Object dtype dtype (‘O’) has no native HDF5 equivalent

So I can´t save the project. When i do it the program don´t save the labels nor the training, just the input images.

Do you think I can do something to fix these errors? Or do I have to traing again the images?

Thank you for your help!!

Hello @LuciaSanchezRuiloba,

first of all, welcome to the community.
I have moved your post to a new topic because I don’t want it to get lost in the original thread.

First of all it should be said that publishing/sharing ilastik projects should (and will) be made easier!

You already found a solution that I would say is suitable - but for some reason does not seem to work.
I have tried duplicating your approach (so I created one project, added labels and exported those labels), created another project, added the data and imported the labels - trained, saved. For me this worked (using the latest beta, 1.4.0b13). What version of ilastik are you using?

Hope we can sort this out quickly

Hi @k-dominik,
Thank you for your answer. Good to know that the solution I found was suitable. I created the initial project with 1.3.3 version. Them I tried to re-train with labels and images with version 1.4.0b13 and I got error messages.
Do you think it could be the different version where I generate the labels. The best way to export labels is in hDF5, isn´t it?
I will try to reproduce this using only the 1.4.0b.13 version just to know if that ws the problem.

Thanks again! Ilastik is great!

Hey @LuciaSanchezRuiloba,

how did you export the labels? Via the export applet, choosing the source “Labels” ?