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Usage

Input data

There are some built-in datasets. For example to get data from a Resolve experiment on mouse liver:

from sparrow.datasets.registry import get_registry

registry=get_registry()
path_image = registry.fetch( "transcriptomics/resolve/mouse/20272_slide1_A1-1_DAPI.tiff" )
path_coordinates = registry.fetch("transcriptomics/resolve/mouse/20272_slide1_A1-1_results.txt")

And to download an example SpatialData object resulting from running the SPArrOW pipeline:

import sparrow as sp
sdata=sp.datasets.resolve_example()

Jupyter notebooks

Check the notebooks in the tutorials section.

Napari plugin

After installing installing SPArrOW, you can run the plugin by first starting Napari, and starting the plugin from Napari's menu bar: napari > Plugins > sparrow.

Use the plugin to tune the parameters of SPArrOW for the different steps of the pipeline. Tuning can be done on small crops of the image. After every step, a corresponding configuration .yaml file will be saved in the output directory chosen by the user. We refer to the hpc documentation for information on how to use these generated configuration files via the CLI.

(Hydra) CLI

Run experiments from the CLI using Hydra. Experiments can be run locally, or on a SLURM cluster.

First copy the configs folder (in the root of this repository) locally, and set the paths to the input data and log directory via the .yaml provided at configs/default.example.yaml. I.e., first rename configs/default.example.yaml to configs/default.yaml and update following fields:

paths:
  log_dir: ${oc.env:HOME}/VIB/DATA/logs/
  data_dir: ${oc.env:HOME}/VIB/DATA/

When running locally, use the following setting for the hydra launcher:

defaults:
  - override /hydra/launcher: submitit_local

If sparrow is run on a SLURM cluster, change this to:

defaults:
  - override /hydra/launcher: submitit_slurm

Next, update configs/dataset/resolve_liver.yaml, with the correct path to the input data, relative to $paths.data_dir set earlier, e.g. the fields:

data_dir: ${paths.data_dir}/resolve/resolve_liver
image: ${dataset.data_dir}/20272_slide1_A1-1_DAPI.tiff
coords: ${dataset.data_dir}/20272_slide1_A1-1_results.txt
markers: ${dataset.data_dir}/markerGeneListMartinNoLow.csv

assuming the RESOLVE mouse liver data is used.

The RESOLVE mouse liver experiment is preconfigured in configs/experiment/resolve_liver.yaml, and can now be run from the CLI:

sparrow +experiment=resolve_liver hydra.searchpath="[/Path/to/local/configs]" task_name=results_sparrow

Please update the hydra.searchpath with the path to the configs folder downloaded locally.

All parameters can also be overwritten from the CLI, e.g. for the size of the min max filter:

sparrow +experiment=resolve_liver hydra.searchpath="[/Path/to/local/configs]" task_name=results_sparrow clean.size_min_max_filter=35

The default values for all parameters for each step of the pipeline can be found at src/sparrow/configs.