The documentation is deployed at Use Ilastik.
This guide demonstrates how to use ilastik to analyze data stored in IDR or an OMERO server.
This repository contains documentation and notebooks.
Running locally:
Finally, if you would like to install the necessary requirements locally, we suggest using Mamba:
- If you do not have any pre-existing conda installation, install Mamba and use mambaforge.
- In case you have a pre-existing conda installation, you can install Mamba by either:
- Using the recommended way to install Mamba from mambaforge. This will not invalidate your conda installation, but possibly your pre-existing conda envs will be in a different location (e.g.
/Users/USER_NAME/opt/anaconda3/envs/) then the new mamba envs (e.g./Users/USER_NAME/mambaforge/envs/). You can verify this by runningconda env list. The addition ofexport CONDA_ENVS_PATH=/Users/user/opt/anaconda3/envs/into your.bashprofileor.zprofilefile will fix this. - Use the Existing conda install way, i.e. run
conda install mamba -n base -c conda-forgewhilst in the base environment. This way can take much longer time than the recommended way described above, and might not lead to a successful installation, especially if run on arm64 (Apple Silicon) OS X.
- Using the recommended way to install Mamba from mambaforge. This will not invalidate your conda installation, but possibly your pre-existing conda envs will be in a different location (e.g.
Create the environment running the commands below as written:
For Windows, OS X x86_64 (NOT arm64 Apple Silicon), Linux:
$ git clone https://github.com/ome/omero-guide-ilastik
$ cd omero-guide-ilastik
$ mamba env create -f binder/environment.yml
For OS X arm64 Apple Silicon
$ git clone https://github.com/ome/omero-guide-ilastik
$ cd omero-guide-ilastik
$ CONDA_SUBDIR=osx-64 mamba env create -f binder/environment.yml
and activate the newly created environment:
$ conda activate omero-guide-ilastik
Before creating a new environment, remember to deactivate the current one:
$ conda deactivate
See also Conda command reference.
The following steps are only required if you want to run the notebooks.
-
If you have Anaconda installed:
- Start Jupyter from the Anaconda-navigator
- To register the environment, run
python -m ipykernel install --user --name omero-guide-ilastik - Select the notebook you wish to run and select the
Kernel>Change kernel>Python [conda env:omero-guide-ilastik]orKernel>Change kernel>omero-guide-ilastik
-
If Anaconda is not installed:
- Open jupyter notebook i.e.
jupyter notebookand select theomero-guide-ilastikkernel or[conda env:omero-guide-ilastik]according to what is available.
To stop the notebook server, in the terminal where te server is running, press
Ctrl C. The following question will be asked in the terminalShutdown this notebook server (y/[n])?. Enter the desired choice. - Open jupyter notebook i.e.
This a Sphinx based documentation.
If you are unfamiliar with Sphinx, we recommend that you first read
[Getting Started with Sphinx](https://docs.readthedocs.io/en/stable/intro/getting-started-with-sphinx.html).