Replies: 5 comments 1 reply
-
Hi Jan, I don't think those are pinned in the repo since they're installed in the docker. @srivarra should be able to comment on the best way to get that running within a conda environment. |
Beta Was this translation helpful? Give feedback.
-
Hey Jan, We have a Conda In your terminal run the following commands to clone the repo and create the environment. git clone -b v0.6.4 https://github.com/angelolab/ark-analysis.git
cd ark-analysis
conda env create -f environment.yml With the In addition the conda environment installs extra notebook dependencies grouped under Let us know if this solves the interactivity issue with the metaclustering GUI. |
Beta Was this translation helpful? Give feedback.
-
Thank you both for the help. I actually installed ark-analysis with conda as you suggested but got ipywidgets 8.0.7, which did not work and produced error: Error displaying widget: model not found |
Beta Was this translation helpful? Give feedback.
-
So I reinstalled the conda environment, with ipywidgets version 8.1.0, but still getting: Error displaying widget: model not found. Probably it is an environment issue. Currently I cannot run the jupyter in docker, otherwise that would be the best option of course. |
Beta Was this translation helpful? Give feedback.
-
What operating system are you using? For example I am able to use the GUI on an Apple Silicon Mac. |
Beta Was this translation helpful? Give feedback.
-
Hi,
firstly, thank you for publishing such an interesting package. We are working on analysis of multiplex immunofluorescence images from COMET and we would be excited to try out your approach for the analysis.
I have segmented an ROI of our image using mesmer and used it as input for the pixel clustering notebook. The jupyter notebook ran well until the GUI part, where I got: Error displaying widget: model not found.
The versions of ipywidgets was: 8.0.7 and jupyterlab_widgets was: 3.0.8
I downgraded to 7.7.0 and 1.1.0 respectively, which I knew would work. Unfortunately, selecting the clusters now does not work. When I click the specified regions, nothing happens. I can still rename the metaclusters though.
I would like to ask, whether you have some minimum version of these packages/ or environment requirements for the selection to work.
Best regards
Jan
Beta Was this translation helpful? Give feedback.
All reactions