Question about H5 output in the imcSegmentation Pipeline about imcsegmentationpipeline

[DenisSch]

I had a similar issue yesterday. The h5 images were just saved in a different directory.

Have you changed the Default Output Folder in View output settings?

[arcolombo]

I am using CellProfiler 2.2.0, should I still be expecting H5s for each image ? Yes under "View output settings" , I have the HF5 option set to the correct output directory. The analysis does generate a single HDF5 file. However, according to the previously posted instructions, should I be expecting an H5 for each image and then upload this into ilastik?

The HDF5 generated by CellProfiler is an HDf5 of the entire project. If I try to entire this HDF5 output by cellProfiler into Ilastik, I receive an error from ilastik stating, "HDF5 file output has no image datasets."

So I am not sure how to generate HDF5s of each image to input into ilastik.

Do I need to be using the module "ExportToCellH5" module?
Thank you again very much

[arcolombo]

well we can close this issue because although the documentation does reference the H5s to be input, it is actually not necessary for ilastik.

[votti]

Hey there,

Please note that this deacribes a new version of the pipeline based on cellprofiller 3.1.5 and some new modules.

I tried to describe the setup step by step in
https://github.com/BodenmillerGroup/ImcSegmentationPipeline/blob/development/scripts/imc_preprocessing.ipynb

It requires the use of thr cp3 pipelines found in this repository in the development branch.
E.g. The 1_prepate_ilastik has now a 'save images as hdf5' module, which creates the output I am refering to!

Note that this will also download some example data.

I would be happy for any feedback!