diff --git a/README.md b/README.md
index bff3d462af8d8071b3594e7a9e5bf170b46cbebb..98c1d5284d17d7d99d74f2d9798e3ff23e89e0bb 100644
--- a/README.md
+++ b/README.md
@@ -20,6 +20,8 @@ See our [installation instructions]( https://aliby.readthedocs.io/en/latest/INST
### CLI
+If installed via poetry, you have access to a Command Line Interface (CLI)
+
```bash
aliby-run --expt_id EXPT_PATH --distributed 4 --tps None
```
@@ -31,6 +33,8 @@ And to run Omero servers, the basic arguments are shown:
The output is a folder with the original logfiles and a set of hdf5 files, one with the results of each multidimensional inside.
+For more information, including available options, see the page on [running the analysis pipeline](https://aliby.readthedocs.io/en/latest/PIPELINE.html)
+
## Using specific components
### Access raw data
diff --git a/docs/source/INSTALL.md b/docs/source/INSTALL.md
index 94abc570f87bc636041e8d9203c7247a782ccd0b..b19b576e29f5d163a009e07d0fa5080608a2ebdc 100644
--- a/docs/source/INSTALL.md
+++ b/docs/source/INSTALL.md
@@ -62,7 +62,7 @@ For Windows, the simplest way to install it is using conda (or mamba). You can i
$ \PATH\TO\POETRY\LOCATION\poetry install
- MacOS
- Under work (See issue https://github.com/ome/omero-py/issues/317)
+ For local access and processing, follow the same instructions as Linux. Remote access to OMERO servers depends on some issues in one of our depedencies being solved (See issue https://github.com/ome/omero-py/issues/317)
### Git version
@@ -71,9 +71,23 @@ Install [ poetry ](https://python-poetry.org/docs/#installation) for dependency
In case you want to have local version:
$ git clone git@gitlab.com/aliby/aliby.git
- $ cd aliby && poetry install --all-extras
+ $ cd aliby
+
+ and then either
-This will automatically install the [ BABY ](https://gitlab.com/aliby/baby) segmentation software. Support for additional segmentation and tracking algorithms is under development.
+ $$ poetry install --all-extras
+
+for everything, including tools to access OMERO servers, or
+
+ $$ poetry install
+
+for a version with only local access, or
+
+ $$ poetry install --with dev
+
+to install with compatible versions of the development tools we use, such as black.
+
+These commands will automatically install the [ BABY ](https://gitlab.com/aliby/baby) segmentation software. Support for additional segmentation and tracking algorithms is under development.
## Omero Server
diff --git a/docs/source/PIPELINE.md b/docs/source/PIPELINE.md
new file mode 100644
index 0000000000000000000000000000000000000000..127ff0c2efc7da40364600db94840c7298a84ce4
--- /dev/null
+++ b/docs/source/PIPELINE.md
@@ -0,0 +1,87 @@
+# Running the analysis pipeline
+
+You can run the analysis pipeline either via the command line interface (CLI) or using a script that incorporates the `aliby.pipeline.Pipeline` object.
+
+## CLI
+
+On a CLI, you can use the `aliby-run` command. This command takes options as follows:
+- `--host`: Address of image-hosting server.
+- `--username`: Username to access image-hosting server.
+- `--password`: Password to access image-hosting server.
+- `--expt_id`: Number ID of experiment stored on host server.
+- `--distributed`: Number of distributed cores to use for segmentation and signal processing. If 0, there is no parallelisation.
+- `--tps`: Optional. Number of time points from the beginning of the experiment to use. If not specified, the pipeline processes all time points.
+- `--directory`: Optional. Parent directory to save the data files (HDF5) generated, `./data` by default; the files will be stored in a child directory whose name is the name of the experiment.
+- `--filter`: Optional. List of positions to use for analysis. Alternatively, a regex (regular expression) or list of regexes to search for positions. **Note: for the CLI, currently it is not able to take a list of strings as input.**
+- `--overwrite`: Optional. Whether to overwrite an existing data directory. True by default.
+- `--override_meta`: Optional. Whether to overwrite an existing data directory. True by default.
+
+Example usage:
+ ```bash
+aliby-run --expt_id EXPT_PATH --distributed 4 --tps None
+ ```
+
+And to run Omero servers, the basic arguments are shown:
+ ```bash
+ aliby-run --expt_id XXX --host SERVER.ADDRESS --user USER --password PASSWORD
+ ```
+
+
+## Script
+
+Use the `aliby.pipeline.Pipeline` object and supply a dictionary, following the example below. The meaning of the parameters are the same as described in the CLI section above.
+
+```python
+#!/usr/bin/env python3
+
+from aliby.pipeline import Pipeline, PipelineParameters
+
+# Specify experiment IDs
+ids = [101, 102]
+
+for i in ids:
+ print(i)
+ try:
+ params = PipelineParameters.default(
+ # Create dictionary to define pipeline parameters.
+ general={
+ "expt_id": i,
+ "distributed": 6,
+ "host": "INSERT ADDRESS HERE",
+ "username": "INSERT USERNAME HERE",
+ "password": "INSERT PASSWORD HERE",
+ # Ensure data will be overwriten
+ "override_meta": True,
+ "overwrite": True,
+ }
+ )
+
+ # Fine-grained control beyond general parameters:
+ # change specific leaf in the extraction tree.
+ # This example tells the pipeline to additionally compute the
+ # nuc_est_conv quantity, which is a measure of the degree of
+ # localisation of a signal in a cell.
+ params = params.to_dict()
+ leaf_to_change = params["extraction"]["tree"]["GFP"]["np_max"]
+ leaf_to_change.add("nuc_est_conv")
+
+ # Regenerate PipelineParameters
+ p = Pipeline(PipelineParameters.from_dict(params))
+
+ # Run pipeline
+ p.run()
+
+ # Error handling
+ except Exception as e:
+ print(e)
+```
+
+This example code can be the contents of a `run.py` file, and you can run it via
+
+```bash
+python run.py
+```
+
+in the appropriate virtual environment.
+
+Alternatively, the example code can be the contents of a cell in a jupyter notebook.