I guess it is obvious in retrospect, but it took me by surprise that I can only use python packages available within Slicer when I use Slicer Jupyter kernel. What is the recommended approach for installing extra python packages to use with Slicer kernel? In my specific case, for example, I would li…

Slicer will switch to Python 3 within days. Then you can install any Python package using pip. Each Slicer installation will act as yet another Python environment. The huge advantage of using Slicer’s embedded Python kernel is that you can continuously use both the desktop and Jupyter interface. Fo…

[image] lassoan: Slicer will switch to Python 3 within days. Then you can install any Python package using pip. I see. I will revisit it then. How reliable is the “within days” estimate? I can wait days, but if I need to wait weeks, then I would rather implement the other solution with the s…

What we end up doing is that instead of having large notebooks that call out to various Python environments, in a project we use a couple of notebooks, and a few environments. Data pre-processing and feature extraction uses Slicer flnotebook, exported data is used for machine learning training using…

Yes, that is exactly what I was planning to do, but I need those other python packages for interacting with the metadata that I want to use in conjunction with image visualization in Slicer.

When I run into similar issues, I use numpy files or csv files to communicate data between Slicer notebooks and Python 3 notebooks. With standard paths and file names, it is not as painful as it sounds. But I’m also looking forward to trying Slicer with Python 3. In a few days, we won’t have these p…

[image] fedorov: How reliable is the “within days” estimate? You can find an update from @jcfr here in this topic: Updating slicer to work with python 3 - #3 by jcfr

Using SlicerJupyter with python packages outside of Slicer distribution

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lassoan (Andras Lasso) March 18, 2019, 5:29am 7

You can find an update from @jcfr here in this topic: Updating slicer to work with python 3 - #3 by jcfr

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Using SlicerJupyter with python packages outside of Slicer distribution

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