README.md

# DEPRECATED AS OF 2023-02-02! -- PROJECT MIGRATED TO https://gitlab.com/aliby/aliby

# ALIBY (Analyser of Live-cell Imaging for Budding Yeast)

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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.

## 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.

For analysing local data
 ```bash
pip install aliby # aliby[network] if you want to access an OMERO server
 ```

See our [installation instructions]( https://aliby.readthedocs.io/en/latest/INSTALL.html ) for more details.

### CLI

 ```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 
 ```

The output is a folder with the original logfiles and a set of hdf5 files, one with the results of each multidimensional inside.

## Using specific components

### Access raw data

ALIBY's tooling can also be used as an interface to OMERO servers, taking care of fetching data when needed.
 ```python
from aliby.io.dataset import Dataset
from aliby.io.image import Image

server_info= {
            "host": "host_address",
            "username": "user",
            "password": "xxxxxx"}
expt_id = XXXX
tps = [0, 1] # Subset of positions to get.

with Dataset(expt_id, **server_info) as conn:
    image_ids = conn.get_images()

#To get the first position
with Image(list(image_ids.values())[0], **server_info) as image:
    dimg = image.data
    imgs = dimg[tps, image.metadata["channels"].index("Brightfield"), 2, ...].compute()
    # tps timepoints, Brightfield channel, z=2, all x,y
```

### Tiling the raw data

A `Tiler` object performs trap registration. It may be built in different ways but the simplest one is using an image and a the default parameters set.

```python
from aliby.tile.tiler import Tiler, TilerParameters
with Image(list(image_ids.values())[0], **server_info) as image:
    tiler = Tiler.from_image(image, TilerParameters.default())
    tiler.run_tp(0)
```

The initialisation should take a few seconds, as it needs to align the images
in time.

It fetches the metadata from the Image object, and uses the TilerParameters values (all Processes in aliby depend on an associated Parameters class, which is in essence a dictionary turned into a class.)

#### Get a timelapse for a given trap
```python
fpath = "h5/location"

trap_id = 9
trange = list(range(0, 30))
ncols = 8

riv = remoteImageViewer(fpath)
trap_tps = riv.get_trap_timepoints(trap_id, trange, ncols)
```

This can take several seconds at the moment.
For a speed-up: take fewer z-positions if you can.

#### Get the traps for a given time point
Alternatively, if you want to get all the traps at a given timepoint:

```python
timepoint = 0
seg_expt.get_tiles_timepoints(timepoint, tile_size=96, channels=None,
                                z=[0,1,2,3,4])
```


### Contributing
See [CONTRIBUTING](https://aliby.readthedocs.io/en/latest/INSTALL.html) on how to help out or get involved.