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Commit 521c25c3 authored by Alán Muñoz's avatar Alán Muñoz
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add cli info

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End-to-end processing of cell microscopy time-lapses. ALIBY automates segmentation, tracking, lineage predictions, post-processing and report production. It leverages the existing Python ecosystem and open-source scientific software available to produce seamless and standardised pipelines. End-to-end processing of cell microscopy time-lapses. ALIBY automates segmentation, tracking, lineage predictions, post-processing and report production. It leverages the existing Python ecosystem and open-source scientific software available to produce seamless and standardised pipelines.
## Quickstart Documentation ## Quickstart Documentation
Installation of [VS Studio](https://visualstudio.microsoft.com/downloads/#microsoft-visual-c-redistributable-for-visual-studio-2022) Native MacOS support for is under work, but you can use containers (e.g., Docker, Podman) in the meantime.
We use (and recommend) [OMERO](https://www.openmicroscopy.org/omero/) to manage our microscopy database, but ALIBY can process both locally-stored experiments and remote ones hosted on a server. For analysing local data
```python
### Setting up a server pip install aliby
For testing and development, the easiest way to set up an OMERO server is by ```
using Docker images.
[The software carpentry](https://software-carpentry.org/) and the [Open
Microscopy Environment](https://www.openmicroscopy.org), have provided
[instructions](https://ome.github.io/training-docker/) to do this.
The `docker-compose.yml` file can be used to create an OMERO server with an
accompanying PostgreSQL database, and an OMERO web server.
It is described in detail
[here](https://ome.github.io/training-docker/12-dockercompose/).
Our version of the `docker-compose.yml` has been adapted from the above to and if you want to use an OMERO server:
use version 5.6 of OMERO. ```python
pip install aliby[network]
```
To start these containers (in background): See our [installation instructions]( https://aliby.readthedocs.io/en/latest/INSTALL.html ) for more details.
```shell script
cd pipeline-core
docker-compose up -d
```
Omit the `-d` to run in foreground.
To stop them, in the same directory, run: ### CLI
```shell script
docker-compose stop
```
### Installation ```bash
aliby-run --expt_id EXPT_PATH --distributed 4 --tps None
```
See our [installation instructions]( https://aliby.readthedocs.io/en/latest/INSTALL.html ) for more details. And to run Omero servers, the basic arguments are shown:
```bash
aliby-run --expt_id XXX --host SERVER.ADDRESS --user USER --password PASSWORD
```
### Raw data access ### Raw data access
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