aliby 0.1.64

Process and analyse live-cell imaging data

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

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 Native MacOS support for is under work, but you can use containers (e.g., Docker, Podman) in the meantime.

To analyse local data

pip install aliby 

Add any of the optional flags omero and utils (e.g., pip install aliby[omero, utils]). omero provides tools to connect with an OMERO server and utils provides visualisation, user interface and additional deep learning tools.

See our installation instructions for more details.

CLI

If installed via poetry, you have access to a Command Line Interface (CLI)

aliby-run --expt_id EXPT_PATH --distributed 4 --tps None

And to run Omero servers, the basic arguments are shown:

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.

For more information, including available options, see the page on running the analysis pipeline

Using specific components

Access raw data

ALIBY's tooling can also be used as an interface to OMERO servers, for example, to fetch a brightfield channel.

from aliby.io.omero import Dataset, 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.

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 tile (remote connection)

fpath = "h5/location"

tile_id = 9
trange = range(0, 10)
ncols = 8

riv = remoteImageViewer(fpath)
trap_tps = [riv.tiler.get_tiles_timepoint(tile_id, t) for t in trange] 

# You can also access labelled traps
m_ts = riv.get_labelled_trap(tile_id=0, tps=[0])

# And plot them directly
riv.plot_labelled_trap(trap_id=0, channels=[0, 1, 2, 3], trange=range(10))

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

Get the tiles for a given time point

Alternatively, if you want to get all the traps at a given timepoint:

timepoint = (4,6)
tiler.get_tiles_timepoint(timepoint, channels=None,
                                z=[0,1,2,3,4])

Contributing

See CONTRIBUTING on how to help out or get involved.