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Python

The steinbock framework can be used programmatically using the steinbock Python package.

In this section, the installation of the steinbock Python package is described.

Requirements

Python 3.8 or newer

Tested versions of Python package dependencies can be found in requirements.txt.

Installation

The steinbock Python package can be installed from PyPI as follows:

pip install steinbock

The following extras are available:

  • imc to enable IMC preprocessing functionality
  • deepcell to enable DeepCell segmentation functionality

To install all extras, use the all extra:

pip install "steinbock[all]"

Package version conflics

Some of the dependencies of steinbock are incompatible due to different version requirements. As a workaround, use the following strategy for installing tested combinations of package versions:

pip install --upgrade deepcell==0.11.0
pip install --upgrade -r requirements.txt
pip install --upgrade "steinbock[all]"

Usage

Please refer to Python usage for usage instructions.

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