This repository contains a notebook for practicals during Advanced methods in bioimage analysis
This repository is intended to be run on https://band.embl.de/ with the following course material available:
$ pwd
/scratch/bioimagecourse2023/session1
$ ls -l
total 146350
drwxr-xr-x 9 josh_openmicroscopy users 4096 Aug 29 15:30 EMBO-Practical-Course-2023
-rw-r--r-- 1 josh_openmicroscopy users 86485611 Aug 20 18:47 Mambaforge-Linux-x86_64.sh
-rw-r----- 1 josh_openmicroscopy users 23433941 Aug 29 10:44 OMEZarrReader-0.3.1-jar-with-dependencies.jar
drwxr-xr-x 4 josh_openmicroscopy users 4096 Aug 21 11:48 conda
drwxr-xr-x 3 josh_openmicroscopy users 4096 Aug 31 09:16 data
drwxr-xr-x 19 josh_openmicroscopy users 4096 Aug 29 14:53 mambaforge
-rwxr-xr-x 1 josh_openmicroscopy users 26406912 Aug 21 12:16 mc
-rw-r--r-- 1 josh_openmicroscopy users 78 Aug 29 11:13 notebook.sh
-rw-r--r-- 1 josh_openmicroscopy users 242 Aug 29 10:47 setup.sh
If you would like to install the necessary requirements locally, we suggest using conda or omamba, e.g.:
https://mamba.readthedocs.io/en/latest/mamba-installation.html#mamba-install
(At the time of the workshop, micromamba did not work with Jupyter.)
Then, to create the environment:
$ git clone git://github.com/ome/EMBO-Practical-Course-2023
$ cd EMBO-Practical-Course-2023
$ omamba create -n embo -f binder/environment.yml
Installing the requirements locally means that you
can then use the tools like bioformats2raw without needing to launch
Jupyter itself:
$ omamba activate embo
$ bioformats2raw my.tiff output
But if you would like, you can run the Notebook server yourself:
$ mamba activate embo
$ jupyter notebook 3_POSIX_Bash.ipynb
Or if you would like to run this repository locally and have Docker installed, you can use the repo2docker tool to run this repository as a local Docker instance:
$ git clone git://github.com/ome/EMBO-Practical-Course-2023
$ cd EMBO-Practical-Course-2023
$ repo2docker .
Then follow the instructions that are printed after the Docker image is built.