A set of Notebooks to demonstrate how to access the images and metadata from OMERO.
To build the image run, in this repository:
$ docker build -t training-notebooks .
The image contains the dependencies required to connect to OMERO 5.5.x.
To start the image in Jupyter:
$ docker run -it -p 8888:8888 training-notebooks
To start the image in Jupyterlab:
$ docker run -it -p 8888:8888 -e JUPYTER_ENABLE_LAB=true training-notebooks
To update a notebook while this is running: In another terminal, get the container ID and copy a notebook e.g. idr0002.ipynb
$ docker ps
$ docker cp CellProfiler/idr0002.ipynb <container_id>:/home/jovyan/notebooks/CellProfiler/idr0002.ipynb
Now refresh the notebook in the browser.
To restart a container and get the URL to open in your browser:
$ docker restart <container_id>
$ docker logs <container_id>
The notebooks in this repository are meant to exemplify how to access data in OMERO.
| Notebook | Lang | Description |
|---|---|---|
| OMERO example | Py | Shows how to connect to OMERO and read data. |
| Calculate Sharpness | Py | Calculates sharpness of images and generates heatmaps. |
| Illumination Correction | Py | Correct the selected image. |
| R-OMERO example | R | Shows how to connect to OMERO and manipulate data using R. |
| idr0021 ROIs | R | Read OMERO.table data, performs some basic statistics on it and create a plot. |
| Statistics Fruit Fly | Py | Process Images stored in OMERO using CellProfiler. |
| idr0002 | Py | Process a plate from idr0002 using CellProfiler. |
| SimpleFRAP | Py | Process a dataset measuring the intensity in a named Channel within a ROI. |
The notebooks have now been copied to other repositories as specified below. The new repositories give the possiblity to run these notebooks using BinderHub. The notebooks in this repository which were copied will be deleted later:
- Notebooks under CellProfiler are now available at omero-guide-cellprofiler.
- Notebooks under ilastik are now available at omero-guide-ilastik.
- Notebooks under Fiji are now available at omero-guide-fiji.
- Notebooks under Orbit are now available at omero-guide-orbit.
- Notebooks under Python are now available at omero-guide-python.
- Notebooks under R are now available at omero-guide-r.