# \#jupyter **URL:** https://forum.qiime2.org/tag/jupyter/136.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Visualization error on Jupyter notebook](https://forum.qiime2.org/t/visualization-error-on-jupyter-notebook/33272)
**Author:** [@kochi](https://forum.qiime2.org/u/kochi)\ **Replies:** 5\ **Last updated:** [June 17, 2025, 6:41am UTC](https://forum.qiime2.org/t/visualization-error-on-jupyter-notebook/33272 "2025-06-17T06:41:21Z")
Hi all, I've used qiime2 for more than 5 years on Intel Mac. Recently, while using qiime2 on Jupyter notebook, I am facing the following error when performing a visualization. As a result, interactive figures are not sh… --- ## [QIIME visualization on a Jupyter Server](https://forum.qiime2.org/t/qiime-visualization-on-a-jupyter-server/33277)
**Author:** [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)\ **Replies:** 1\ **Last updated:** [June 9, 2025, 6:40pm UTC](https://forum.qiime2.org/t/qiime-visualization-on-a-jupyter-server/33277 "2025-06-09T18:40:44Z")
Hi All, I'm trying to use QIIME within a Jupyter Hub server instance from docker. I cannot get the jupyter serverextension enable --py qiime2 --sys-prefix to work. I've tried adding it various places in the docker build… --- ## [Exporting barplot to .qzv from python API](https://forum.qiime2.org/t/exporting-barplot-to-qzv-from-python-api/29871)
**Author:** [@sklasek](https://forum.qiime2.org/u/sklasek)\ **Replies:** 3\ **Last updated:** [April 12, 2024, 7:40pm UTC](https://forum.qiime2.org/t/exporting-barplot-to-qzv-from-python-api/29871 "2024-04-12T19:40:25Z")
Hello, I'm a new qiime user trying to make and view a taxonomy barplot within the python API in a jupyter notebook. I've imported FeatureTable\[Frequency\] and featureData\[Taxonomy\] objects and created a barplot with them… --- ## [Installing Qiime2 extension under JupyterLab 4.x.x](https://forum.qiime2.org/t/installing-qiime2-extension-under-jupyterlab-4-x-x/29616)
**Author:** [@Michal\_Kowalski](https://forum.qiime2.org/u/Michal_Kowalski)\ **Replies:** 3\ **Last updated:** [March 20, 2024, 6:12pm UTC](https://forum.qiime2.org/t/installing-qiime2-extension-under-jupyterlab-4-x-x/29616 "2024-03-20T18:12:44Z")
Hi! I'm encountering challenges integrating QIIME 2 (version 2024.2, installed via conda) with JupyterHub, which is running as a system service in a separate conda environment. My goal is to use QIIME 2's functionalitie… --- ## [Taxonomy table looked different in R than when it was opened in QIIME (missing taxon level prefix)?](https://forum.qiime2.org/t/taxonomy-table-looked-different-in-r-than-when-it-was-opened-in-qiime-missing-taxon-level-prefix/23205)
**Author:** [@Diki](https://forum.qiime2.org/u/Diki)\ **Replies:** 3\ **Last updated:** [June 1, 2022, 1:00pm UTC](https://forum.qiime2.org/t/taxonomy-table-looked-different-in-r-than-when-it-was-opened-in-qiime-missing-taxon-level-prefix/23205 "2022-06-01T13:00:15Z")
Hi, I ran QIIME2 for my raw reads via jupyter using %%bash in the shared Mac for heavy analysis (also a little Python for data viz). After that, we copied several outputs to build a phyloseq object in our personal compu… --- ## [JupyterHub: "jupyter serverextension enable --py qiime2 --sys-prefix" does not work](https://forum.qiime2.org/t/jupyterhub-jupyter-serverextension-enable-py-qiime2-sys-prefix-does-not-work/20846)
**Author:** [@jaehyun.kim](https://forum.qiime2.org/u/jaehyun.kim)\ **Replies:** 2\ **Last updated:** [September 25, 2021, 11:12am UTC](https://forum.qiime2.org/t/jupyterhub-jupyter-serverextension-enable-py-qiime2-sys-prefix-does-not-work/20846 "2021-09-25T11:12:14Z")
Hi all, I built the JupyterHub environment considering hosting a small teaching session. The QIIME 2 is isntalled in a separate conda env and it works well. When an external user logs in to the JupyterHub and runs the … --- ## [Jupyter lab/notebook in Qiime 2 (v. 2021.4)](https://forum.qiime2.org/t/jupyter-lab-notebook-in-qiime-2-v-2021-4/20182)
**Author:** [@Shannon\_Wilson](https://forum.qiime2.org/u/Shannon_Wilson)\ **Replies:** 2\ **Last updated:** [July 13, 2021, 8:36pm UTC](https://forum.qiime2.org/t/jupyter-lab-notebook-in-qiime-2-v-2021-4/20182 "2021-07-13T20:36:50Z")
This is likely a stupid question, but I have spent hours now trolling the forum and the web for answers and nothing seems to work for me. I am VERY new to coding and trying to figure out how to use jupyter notebooks in … --- ## [Using qiime tools view in jupyter](https://forum.qiime2.org/t/using-qiime-tools-view-in-jupyter/17463)
**Author:** [@asajoh](https://forum.qiime2.org/u/asajoh)\ **Replies:** 4\ **Last updated:** [November 16, 2020, 12:09pm UTC](https://forum.qiime2.org/t/using-qiime-tools-view-in-jupyter/17463 "2020-11-16T12:09:00Z")
When using ´qiime tools view somefilename.qzv´ in jupyter it opens up nicely in a new browser window, so no problems there. However, I am unable to then move on because I can't get the cell to stop working. There is a to… --- ## [Activating JupyterLab in Qiime2](https://forum.qiime2.org/t/activating-jupyterlab-in-qiime2/9697)
**Author:** [@laura.d](https://forum.qiime2.org/u/laura.d)\ **Replies:** 11\ **Last updated:** [May 13, 2019, 4:34am UTC](https://forum.qiime2.org/t/activating-jupyterlab-in-qiime2/9697 "2019-05-13T04:34:12Z")
Hi, Please can you provide details on how to run JupyterLab within Qiime2. I have qiime2 2018-11 installed via conda. I activated my qiime2 environment and did a conda install of the JupyterLab packages (conda install… --- ## [QIIME and R Jupyter Kernel?](https://forum.qiime2.org/t/qiime-and-r-jupyter-kernel/6912)
**Author:** [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)\ **Replies:** 0\ **Last updated:** [November 12, 2018, 4:46pm UTC](https://forum.qiime2.org/t/qiime-and-r-jupyter-kernel/6912 "2018-11-12T16:46:18Z")
Hi all, Im not sure where the best place is to put this, but I figure this is as good as anywhere, in the hopes that someone else has been more successful that I have, or that I can save someone else from two days with … --- ## [Qiime feature-table rarefy?](https://forum.qiime2.org/t/qiime-feature-table-rarefy/2645)
**Author:** [@talderete](https://forum.qiime2.org/u/talderete)\ **Replies:** 1\ **Last updated:** [January 19, 2018, 8:15pm UTC](https://forum.qiime2.org/t/qiime-feature-table-rarefy/2645 "2018-01-19T20:15:20Z")
Hello! I am trying to use the qiime feature-table rarefy plugin and receive an error when executing the code below. #code qiime feature-table rarefy --i-table deblur-seqs-tax-.qza \\ --p-sampling-depth 400 --o-rar… --- ## [Tutorial of Artifact API on the qiime2 website](https://forum.qiime2.org/t/tutorial-of-artifact-api-on-the-qiime2-website/2608)
**Author:** [@SabuTheCavy](https://forum.qiime2.org/u/SabuTheCavy)\ **Replies:** 1\ **Last updated:** [January 17, 2018, 5:28pm UTC](https://forum.qiime2.org/t/tutorial-of-artifact-api-on-the-qiime2-website/2608 "2018-01-17T17:28:25Z")
Hi All, I just start to learn Python and Jupyter notebook and tried to follow the tutorials on the Qiime2 official website. I installed qiime2-2017.12 for macOS within a conda environment under the ANACONDA NAVIGATOR. … --- ## [Qiime2 on AWS - can't access Jupyter Notebook](https://forum.qiime2.org/t/qiime2-on-aws-cant-access-jupyter-notebook/2007)
**Author:** [@Gil\_Sharon](https://forum.qiime2.org/u/Gil_Sharon)\ **Replies:** 2\ **Last updated:** [November 29, 2017, 8:21pm UTC](https://forum.qiime2.org/t/qiime2-on-aws-cant-access-jupyter-notebook/2007 "2017-11-29T20:21:24Z")
Hi all, Trying to set up Qiime2 2017.10 on AWS using the community ami. all went well, except it cant access the notebook server. I have port 8888 (TCP) open, so I don't think that's the problem. when I run jupyter not…