# \#jupyter

**URL:** https://discourse.slicer.org/tag/jupyter/155.md

[Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md)

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## [My Kernel keeps dying - Slicer 4.11 - Jupyter](https://discourse.slicer.org/t/my-kernel-keeps-dying-slicer-4-11-jupyter/40902)

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**Author:** [@Saladi](https://discourse.slicer.org/u/Saladi)\
**Replies:** 2\
**Last updated:** [December 30, 2024, 9:15am UTC](https://discourse.slicer.org/t/my-kernel-keeps-dying-slicer-4-11-jupyter/40902 "2024-12-30T09:15:55Z")

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Hi all, I am using Slicer 4.11 rn. I am trying to run the juypter server. But i keep getting this error: " Building wheel for pywinpty (PEP 517): started WARNING: Subprocess output does not appear to be encoded as …

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## [How can jupyter control all the slicer](https://discourse.slicer.org/t/how-can-jupyter-control-all-the-slicer/39592)

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**Author:** [@VirOrange](https://discourse.slicer.org/u/VirOrange)\
**Replies:** 2\
**Last updated:** [October 12, 2024, 1:34pm UTC](https://discourse.slicer.org/t/how-can-jupyter-control-all-the-slicer/39592 "2024-10-12T13:34:42Z")

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Hi everyone, I am new to Slicer and would like to understand how Jupyter can be used to control Slicer. Specifically: Does using Jupyter mean that I can debug and trace the execution of different modules within Slicer…

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## [Example Jupyter notebook not compatible with slicer 5.6](https://discourse.slicer.org/t/example-jupyter-notebook-not-compatible-with-slicer-5-6/35121)

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**Author:** [@Matteboo](https://discourse.slicer.org/u/Matteboo)\
**Replies:** 1\
**Last updated:** [March 27, 2024, 1:13pm UTC](https://discourse.slicer.org/t/example-jupyter-notebook-not-compatible-with-slicer-5-6/35121 "2024-03-27T13:13:23Z")

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Hello, I started to learn how to use slicer from Jupyter. I’ve used the example notebook provided here GitHub - Slicer/SlicerNotebooks: Examples that illustrate how to use 3D Slicer via Jupyter notebooks in Python Howe…

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## [Using slicer as a Jupyter kernel, how to set up a variable inspector](https://discourse.slicer.org/t/using-slicer-as-a-jupyter-kernel-how-to-set-up-a-variable-inspector/35054)

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**Author:** [@Matteboo](https://discourse.slicer.org/u/Matteboo)\
**Replies:** 0\
**Last updated:** [March 25, 2024, 1:51pm UTC](https://discourse.slicer.org/t/using-slicer-as-a-jupyter-kernel-how-to-set-up-a-variable-inspector/35054 "2024-03-25T13:51:43Z")

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Hello, I recently started to use Slicer as a Jupyter kernel. I’m setting up the environment and I’m trying to set up a variable inspector. I installed this extension however, it’s not working. When I launch a noteb…

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## [3dslicer v5.4.0, not able to download the slicerjupter-extension from developer tools](https://discourse.slicer.org/t/3dslicer-v5-4-0-not-able-to-download-the-slicerjupter-extension-from-developer-tools/32211)

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**Author:** [@palak](https://discourse.slicer.org/u/palak)\
**Replies:** 1\
**Last updated:** [October 18, 2023, 10:40am UTC](https://discourse.slicer.org/t/3dslicer-v5-4-0-not-able-to-download-the-slicerjupter-extension-from-developer-tools/32211 "2023-10-18T10:40:58Z")

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not able to download the slicer jupyter extension, getting error: Failed downloading: https://slicer-packages.kitware.com/api/v1/file/64e0fcdb06a93d6cff366315/download

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## [Error displaying widget: model not found](https://discourse.slicer.org/t/error-displaying-widget-model-not-found/29696)

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**Author:** [@morning\_jade](https://discourse.slicer.org/u/morning_jade)\
**Replies:** 6\
**Last updated:** [September 12, 2023, 11:35pm UTC](https://discourse.slicer.org/t/error-displaying-widget-model-not-found/29696 "2023-09-12T23:35:04Z")

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When I use jupyter to run code： slicernb. ViewInteractiveWidget()，Widget failed to load and reported an error Error displaying widget: model not found and 3d slicer shows error \[I 2023-05-28 16:55:56.680 ServerApp\] Co…

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## [Slicer kernel for jupyter notebook and python debugger setup in vscode](https://discourse.slicer.org/t/slicer-kernel-for-jupyter-notebook-and-python-debugger-setup-in-vscode/26087)

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**Author:** [@wRossw](https://discourse.slicer.org/u/wRossw)\
**Replies:** 6\
**Last updated:** [November 12, 2022, 4:18am UTC](https://discourse.slicer.org/t/slicer-kernel-for-jupyter-notebook-and-python-debugger-setup-in-vscode/26087 "2022-11-12T04:18:03Z")

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Hi, I have a few questions for getting a working setup of the jupyter notebook extension and Slicer working within VSCode. I’m still fairly new to making the switch from MATLAB to python, so some of these may be fairly …

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## [Load DICOM in Slicer UI and in Jupyter Docker container](https://discourse.slicer.org/t/load-dicom-in-slicer-ui-and-in-jupyter-docker-container/25372)

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**Author:** [@Katya\_Stansfield](https://discourse.slicer.org/u/Katya_Stansfield)\
**Replies:** 0\
**Last updated:** [September 21, 2022, 9:31am UTC](https://discourse.slicer.org/t/load-dicom-in-slicer-ui-and-in-jupyter-docker-container/25372 "2022-09-21T09:31:26Z")

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Hello – may I please ask for some guidance in using Slicer via Jupyter in a Docker container? I am trying to load some of my DICOM data files, which load with no problem in a local Slicer UI However, when I follow in…

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## [Slicer windows in a custom web application](https://discourse.slicer.org/t/slicer-windows-in-a-custom-web-application/24706)

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**Author:** [@NaglisR](https://discourse.slicer.org/u/NaglisR)\
**Replies:** 5\
**Last updated:** [August 11, 2022, 2:20pm UTC](https://discourse.slicer.org/t/slicer-windows-in-a-custom-web-application/24706 "2022-08-11T14:20:15Z")

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Hi all, I have a somewhat abstract question regarding integrating slicer windows in a custom web application window. Generally I suppose it should work something like this https://youtu.be/vTGQMDIqL9k meaning that the Sl…

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## [Possible malfunction with Slicer kernel for Jupyter notebook?](https://discourse.slicer.org/t/possible-malfunction-with-slicer-kernel-for-jupyter-notebook/24163)

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**Author:** [@KateDelb](https://discourse.slicer.org/u/KateDelb)\
**Replies:** 0\
**Last updated:** [July 3, 2022, 3:00pm UTC](https://discourse.slicer.org/t/possible-malfunction-with-slicer-kernel-for-jupyter-notebook/24163 "2022-07-03T15:00:15Z")

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Hi! I’m trying to import the sitkUtils package in Jupyter notebook, I’m using the 3dSlicer kernel, which has worked perfectly for me before: import sitkUtils as su In a following cell I check if su is imported, which …

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## [How to setup Jupyter Desktop Server](https://discourse.slicer.org/t/how-to-setup-jupyter-desktop-server/23455)

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**Author:** [@Tiago\_Guiomar](https://discourse.slicer.org/u/Tiago_Guiomar)\
**Replies:** 0\
**Last updated:** [May 17, 2022, 1:03pm UTC](https://discourse.slicer.org/t/how-to-setup-jupyter-desktop-server/23455 "2022-05-17T13:03:32Z")

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I’m trying to show the GUI in my jupyter notebook but I need to setup the Jupyter Desktop Server, any idea on how to do it?

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## [Loading nrrd data in python Jupyter notebook script](https://discourse.slicer.org/t/loading-nrrd-data-in-python-jupyter-notebook-script/22637)

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**Author:** [@Hanne1234](https://discourse.slicer.org/u/Hanne1234)\
**Replies:** 7\
**Last updated:** [April 12, 2022, 4:49pm UTC](https://discourse.slicer.org/t/loading-nrrd-data-in-python-jupyter-notebook-script/22637 "2022-04-12T16:49:51Z")

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Hi, I am new working with the PyRadiomics package and I have a very basic question. How to load in the data in the Jupyter Notebook script? I used 3D slicer to perform a segmentation on a PET image and I want to load t…

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## [3D slicer using Jupyter notebook on cloud](https://discourse.slicer.org/t/3d-slicer-using-jupyter-notebook-on-cloud/21827)

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**Author:** [@kianoosh\_kargar](https://discourse.slicer.org/u/kianoosh_kargar)\
**Replies:** 2\
**Last updated:** [February 15, 2022, 2:34pm UTC](https://discourse.slicer.org/t/3d-slicer-using-jupyter-notebook-on-cloud/21827 "2022-02-15T14:34:14Z")

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I found that I couldn’t install 3D slicer on my local pc, but I am able to run it on binder from here: But I want to know that is there any tutorial for using 3D Slicer in a jupyter notebook? Is there any difference be…

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## [How to install python packages using jupyterlab?](https://discourse.slicer.org/t/how-to-install-python-packages-using-jupyterlab/21343)

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**Author:** [@user4](https://discourse.slicer.org/u/user4)\
**Replies:** 4\
**Last updated:** [January 7, 2022, 8:31am UTC](https://discourse.slicer.org/t/how-to-install-python-packages-using-jupyterlab/21343 "2022-01-07T08:31:51Z")

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Hi all,I am using the Slicer 4.11 and I am stucked with installing packages. Here is the thing in detail: I was trying to install some packages,say matplotlib in Slicer: Also,I tried to install the package in Pyt…

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## [Run Slicer in your web browser - as a Jupyter notebook or as a full application](https://discourse.slicer.org/t/run-slicer-in-your-web-browser-as-a-jupyter-notebook-or-as-a-full-application/11569)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 10\
**Last updated:** [December 9, 2021, 10:20am UTC](https://discourse.slicer.org/t/run-slicer-in-your-web-browser-as-a-jupyter-notebook-or-as-a-full-application/11569 "2021-12-09T10:20:24Z")

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It has been possible to use Slicer from Jupyter notebooks but the most recent Slicer Preview Release takes this to a whole new level. Click here to try a few example interactive notebooks now - or see a short video demo…

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## [Is SlicerJupyter broken on macOS due to argon2-cffi (again?)](https://discourse.slicer.org/t/is-slicerjupyter-broken-on-macos-due-to-argon2-cffi-again/15823)

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**Author:** [@pll\_llq](https://discourse.slicer.org/u/pll_llq)\
**Replies:** 24\
**Last updated:** [September 5, 2021, 7:39pm UTC](https://discourse.slicer.org/t/is-slicerjupyter-broken-on-macos-due-to-argon2-cffi-again/15823 "2021-09-05T19:39:07Z")

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Hi, This problem was mentioned here on the forum a couple of times already and some fixes that were made actually worked just a month ago. Forum posts: Commit that addressed the issue I was using Jupyter Lab insi…

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## [Calling module with slicer functions fail in Jupyter notebook](https://discourse.slicer.org/t/calling-module-with-slicer-functions-fail-in-jupyter-notebook/17712)

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**Author:** [@mc\_barbour](https://discourse.slicer.org/u/mc_barbour)\
**Replies:** 3\
**Last updated:** [May 20, 2021, 7:32pm UTC](https://discourse.slicer.org/t/calling-module-with-slicer-functions-fail-in-jupyter-notebook/17712 "2021-05-20T19:32:15Z")

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I’m currently using slicer via jupyter. I’ve written a number of functions to help me batch segment 4dct data and I’m attempting to load those functions into my notebook via a module as I’ve got multiple patients to eval…

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## [Quit Jupyter notebook without shutting down Slicer kernal - Slicer instance is persisting](https://discourse.slicer.org/t/quit-jupyter-notebook-without-shutting-down-slicer-kernal-slicer-instance-is-persisting/16587)

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**Author:** [@Carly\_L](https://discourse.slicer.org/u/Carly_L)\
**Replies:** 2\
**Last updated:** [March 26, 2021, 4:07pm UTC](https://discourse.slicer.org/t/quit-jupyter-notebook-without-shutting-down-slicer-kernal-slicer-instance-is-persisting/16587 "2021-03-26T16:07:17Z")

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Hello, I was running a Jupyter notebook script connected to a Slicer kernel. I accidentally quite the instance of Jupyter notebook (closed out of the window in browser) without first shutting down the Slicer kernel. Now…

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## [Problem with ViewInteractiveWidget - no output visible](https://discourse.slicer.org/t/problem-with-viewinteractivewidget-no-output-visible/14962)

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**Author:** [@seaninko](https://discourse.slicer.org/u/seaninko)\
**Replies:** 4\
**Last updated:** [December 22, 2020, 9:01am UTC](https://discourse.slicer.org/t/problem-with-viewinteractivewidget-no-output-visible/14962 "2020-12-22T09:01:15Z")

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Hello, I have a problem with ViewInteractiveWidget method. It works fine when I launch jupyter server within Slicer, but when I use an external jupyter server it just shows the empty output cell without any rendering. N…

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## [Problems running SlicerJupyter on MacOS](https://discourse.slicer.org/t/problems-running-slicerjupyter-on-macos/15082)

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**Author:** [@jsalas424](https://discourse.slicer.org/u/jsalas424)\
**Replies:** 6\
**Last updated:** [December 21, 2020, 4:11pm UTC](https://discourse.slicer.org/t/problems-running-slicerjupyter-on-macos/15082 "2020-12-21T16:11:36Z")

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I was trying to get the app working by following the instructions here: GitHub - Slicer/SlicerJupyter: Extension for 3D Slicer that allows the application to be used from Jupyter notebook I started the Jupyter Server fr…

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## [Slicer and jupyter kernel dies repeatedly, problem with connection.](https://discourse.slicer.org/t/slicer-and-jupyter-kernel-dies-repeatedly-problem-with-connection/14965)

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**Author:** [@coconutattitude](https://discourse.slicer.org/u/coconutattitude)\
**Replies:** 22\
**Last updated:** [December 10, 2020, 7:56pm UTC](https://discourse.slicer.org/t/slicer-and-jupyter-kernel-dies-repeatedly-problem-with-connection/14965 "2020-12-10T19:56:33Z")

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When I install SlicerJupyter and run it, it tries to connect and the dies. The messsage ist: “The kernel appears to have died. It will restart automatically.” It then restarts and dies again. This happens both when I’m …

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## [Segmentation in Jupyter notebook](https://discourse.slicer.org/t/segmentation-in-jupyter-notebook/13583)

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**Author:** [@Hugo](https://discourse.slicer.org/u/Hugo)\
**Replies:** 5\
**Last updated:** [September 22, 2020, 12:18pm UTC](https://discourse.slicer.org/t/segmentation-in-jupyter-notebook/13583 "2020-09-22T12:18:38Z")

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Hello everyone, I’m trying to make a simply version of 3d slicer using the Jupyter notebook. I would like to enable the « sphere » brush option and be able to choose the % of the brush in my def paint but didn’t find a…

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## [Slicer/Jupyter integration: installing python packages](https://discourse.slicer.org/t/slicer-jupyter-integration-installing-python-packages/13386)

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**Author:** [@yoomi](https://discourse.slicer.org/u/yoomi)\
**Replies:** 29\
**Last updated:** [September 17, 2020, 2:07am UTC](https://discourse.slicer.org/t/slicer-jupyter-integration-installing-python-packages/13386 "2020-09-17T02:07:17Z")

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Hello, I’m having trouble integrating 3D Slicer with Jupyter on my computer. I installed both Slicer and Jupyter, but am stuck on installing python packages. When I paste the below into the python interactor in Slicer a…

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## [Issue creating binder repository to share Slicer notebooks (Wrong Kernel)](https://discourse.slicer.org/t/issue-creating-binder-repository-to-share-slicer-notebooks-wrong-kernel/13139)

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**Author:** [@allihuwa](https://discourse.slicer.org/u/allihuwa)\
**Replies:** 1\
**Last updated:** [August 24, 2020, 2:01pm UTC](https://discourse.slicer.org/t/issue-creating-binder-repository-to-share-slicer-notebooks-wrong-kernel/13139 "2020-08-24T14:01:15Z")

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Hello, I am trying to run my Github repository via binder to be able to share my slicer notebook files (.ipynb) with other people. I am able to create the binder repository but when I open up a .ipynb file the default k…

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## [JupyterNotebooksLib Slicer - functions to edit volume rendering parameters?](https://discourse.slicer.org/t/jupyternotebookslib-slicer-functions-to-edit-volume-rendering-parameters/12776)

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**Author:** [@allihuwa](https://discourse.slicer.org/u/allihuwa)\
**Replies:** 0\
**Last updated:** [July 29, 2020, 9:19pm UTC](https://discourse.slicer.org/t/jupyternotebookslib-slicer-functions-to-edit-volume-rendering-parameters/12776 "2020-07-29T21:19:10Z")

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Hi, I am able to successfully load a volume into the SlicerWeb extension and use the JupyterNotebookLib. What I wanted to do now is use functions in this library that enable me to change the volume rendering presets and …

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## [Issues loading own nrrd file into SlicerWeb Jupyter(Binder tutorial)](https://discourse.slicer.org/t/issues-loading-own-nrrd-file-into-slicerweb-jupyter-binder-tutorial/12679)

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**Author:** [@allihuwa](https://discourse.slicer.org/u/allihuwa)\
**Replies:** 2\
**Last updated:** [July 23, 2020, 10:11am UTC](https://discourse.slicer.org/t/issues-loading-own-nrrd-file-into-slicerweb-jupyter-binder-tutorial/12679 "2020-07-23T10:11:29Z")

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Hello, I am trying to load my own nrrd file to be able to manipulate a volume rendering through the slicerweb notebook extension that runs on jupyter. I am trying to change this example code given on this tutorial: …

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## [How to archive jupyter notebooks](https://discourse.slicer.org/t/how-to-archive-jupyter-notebooks/12239)

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**Author:** [@ungi](https://discourse.slicer.org/u/ungi)\
**Replies:** 3\
**Last updated:** [June 27, 2020, 6:38pm UTC](https://discourse.slicer.org/t/how-to-archive-jupyter-notebooks/12239 "2020-06-27T18:38:20Z")

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I use SlicerJupyter to run automated experiments with Slicer, generating snapshots of the views. Sometimes I forget to save the notebook with valuable results. For non-Slicer notebooks, I can use an external process to s…

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## [Error when running sample Slicer Jupyter Notebooks from local linux machine](https://discourse.slicer.org/t/error-when-running-sample-slicer-jupyter-notebooks-from-local-linux-machine/11975)

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**Author:** [@Andrius](https://discourse.slicer.org/u/Andrius)\
**Replies:** 0\
**Last updated:** [June 10, 2020, 7:29am UTC](https://discourse.slicer.org/t/error-when-running-sample-slicer-jupyter-notebooks-from-local-linux-machine/11975 "2020-06-10T07:29:29Z")

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Dear Slicers, I am just getting started with Python and slicer. My goal is to use slicer to combine ITK, VTK and VMTK capabilities for vascular segmentation and geometric data extraction. I love the idea that all this c…

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## [How to start Slicer Jupyter kernel?](https://discourse.slicer.org/t/how-to-start-slicer-jupyter-kernel/3855)

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**Author:** [@Saima](https://discourse.slicer.org/u/Saima)\
**Replies:** 31\
**Last updated:** [July 11, 2019, 2:21pm UTC](https://discourse.slicer.org/t/how-to-start-slicer-jupyter-kernel/3855 "2019-07-11T14:21:31Z")

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Dear Andras, I installed the JupyterKernel but I receive error output as below: Then I launched jupyter through anaconda. it looks like as below: I have 4.9 nighly version of slicer which I dont see here. Pleas…

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## [Using SlicerJupyter with python packages outside of Slicer distribution](https://discourse.slicer.org/t/using-slicerjupyter-with-python-packages-outside-of-slicer-distribution/6162)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 6\
**Last updated:** [March 18, 2019, 5:29am UTC](https://discourse.slicer.org/t/using-slicerjupyter-with-python-packages-outside-of-slicer-distribution/6162 "2019-03-18T05:29:01Z")

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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 p…

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