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

Support

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

Topic		Replies	Views
Slicer in a python pipeline (but not in the slicer python interpretor) Development	1	358	August 10, 2022
Jupyter notebooks are now usable in 3D Slicer Support feature , python , jupyter	5	5204	October 17, 2018
Slicer/Jupyter integration: installing python packages Support jupyter	29	2665	September 17, 2020
How to start Slicer Jupyter kernel? Support jupyter	31	4356	July 11, 2019
Importing slicer libraries separately, outside embedded Python, like in Conda or Jupiter environments Support	1	675	December 29, 2019

Using SlicerJupyter with python packages outside of Slicer distribution

Related topics