https://github.com/ome/embo-practical-course-2023
Advanced methods in bioimage analysis
https://github.com/ome/embo-practical-course-2023
cloud ngff ome ome-ngff ome-tiff ome-zarr posix s3 training zarr
Last synced: 11 months ago
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Advanced methods in bioimage analysis
- Host: GitHub
- URL: https://github.com/ome/embo-practical-course-2023
- Owner: ome
- License: gpl-3.0
- Created: 2023-08-21T11:27:22.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2023-09-10T15:36:11.000Z (over 2 years ago)
- Last Synced: 2025-06-23T00:32:22.885Z (11 months ago)
- Topics: cloud, ngff, ome, ome-ngff, ome-tiff, ome-zarr, posix, s3, training, zarr
- Language: Jupyter Notebook
- Homepage: https://www.embl.org/about/info/course-and-conference-office/events/bia23-01/
- Size: 8.88 MB
- Stars: 6
- Watchers: 2
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# EMBO Practical Course 2023
This repository contains a notebook for practicals during
[Advanced methods in bioimage analysis](https://www.embl.org/about/info/course-and-conference-office/events/bia23-01/)
## Requirements
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
```
## Running locally
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
## Running in Docker
Or if you would like to run this repository locally and have Docker installed,
you can use the [repo2docker](https://repo2docker.readthedocs.io/en/latest/)
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.