imaxt-mosaic 1.15.0

Image stitching

IMAXT Mosaic Pipeline

The IMAXT mosaic pipeline produces stitched images from tile observations. Currently we support two instruments: Serial Two-Photon Tomography (STPT) and AXIOScan.

Note that raw data (typically in the form of TIFF images) need to be converted to Zarr format first using e.g. stpt2zarr or axio2zarr.

Pipeline Definition File

In order to run the pipeline you need a YAML file as follows:

version: 1

name: imaxt-mosaic

input_path: /storage/imaxt/raw/stpt/20211020_PDX_STG139_GFP_029621_100x15um
output_path: /storage/imaxt/processed/stpt/20211020_PDX_STG139_GFP_029621_100x15um

stitcher: stpt

recipes:
  - calibration
  - mosaic
  - beadfit

resources:
  cpu: 16
  workers: 1
  memory: 48

Execute locally with Owl

In order to run the pipeline locally, install as follows:

pip install imaxt-mosaic owl-pipeline-client

and execute:

owl execute pipeline.yaml

Remote execution

To execute the pipeline using a remote Owl server it is not needed to install the module locally. Just submit as:

owl submit pipeline.yaml