README.md

Pipeline core

The core classes and methods for the python microfluidics, microscopy, and analysis pipeline.

Installation

See INSTALL.md for installation instructions.

Quickstart Documentation

Setting up a server

For testing and development, the easiest way to set up an OMERO server is by using Docker images. The software carpentry and the Open Microscopy Environment, have provided instructions 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.

Our version of the docker-compose.yml has been adapted from the above to use version 5.6 of OMERO.

To start these containers (in background):

cd pipeline-core
docker-compose up -d

Omit the -d to run in foreground.

To stop them, in the same directory, run:

docker-compose stop

Raw data access

from argo.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 is built in different ways, the easiest one is using an image and a the default parameters set.

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

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