Importing multiframe tiff file in ilastik for image segmentation

Hello,

I am trying to import a multiframe tiff file in ilastik.

You only choose a single file. If your stack is contained in a single file (e.g. a multi-page tiff) please use the “Add File” button.


May I know how to import multipage tiff? I couldn’t locate Add file button.

From here (https://www.ilastik.org/documentation/basics/batch#:~:text=When%20clicking%20on%20the%20Add,images%20have%20to%20be%20processed.) I see Add file is avaialble in Batch Prediction input selection.

Which option has to be selected from the below?

I was going through the steps described for image segmentation using ilastik in this repository.

The pixel classication tool was trained for at least 30 mins using all 37 default image filters with each of the pre-processed nuclei, blood vessel and micrometastasis images. Once satisfactory performance was seen for the binary segmentation of each of the nuclei, blood vessel and micrometastasis channels this segmentation was batch applied to other images aquired from the same tissue and animal. The output is a labelled segmetnated images of each of the nuclei, blood vessel and micrometastasis channels as multipage tiff files.

And I am trying to import the multiframe tiff to carry out the above workflow.

Any suggestions on how to import tiff?

I have followed the suggestions offered here and tried to save the multipage tiff
in hdf5 format. The exported file is also a single file. Now when I import the hdf5 file in ilastik,

I couldn’t understand what’s the pattern that has to be entered in the field marked with *. Any suggestions will be really helpful.

Hi @Deepa,

thank you for your patience.

In both cases (with the .tif file and the .h5 file) you can go by the first option add separate image(s)…. That is the one to use whenever your image is in a single file. Sorrry for the confusion.

I would recommend converting to h5 and then opening it via this first option of the Add New button.
I have also tried importing the tif directly and first of all ilastik does not recognize the axes properly (it will import it as a time series - but that can be corrected via the dataset properties. However, performance when using the h5 file is really much much better!

Cheers and let us know if it worked!

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Hi @k-dominik

Thank you very much for your response. I could successfully save the tif file in .h5 format and import
the same.

I’ve got a few more questons

The source file is available, here. I would like to perform image segmentation on this input in ilastik. I’m following the steps documented in this link. the source file has been pre-processed in MATLAB to normalize the flourescent intensities before carrying out image segmentation in ilastik.

I would like to know if the normalization can be done directly in ilastik ( similar to the pre-processing
feature normalization available here).

Referring to this post, I think normalization is it required if one has to use same annotation for all slices.
For instance, in my dataset I have defined the annotation on a single slicer (please check this post).