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. |