hcr-cell-typist 0.1.1

A library to aid cell type classification in HCR experiments, downstream of QuPath

Cell Typist

A library to aid cell type classification in HCR experiments, downstream of QuPath

Installation

We recommend installing all the required dependencies through Miniconda, allowing Cell Typist to run inside a dedicated environment without interfering or causing conflicts with the host computer.

To create a dedicated environment, run the commands below commands inside Anaconda Prompt (on Windows) or a terminal on Linux and macOS.

(base) $ conda create -n ct python=3.12
(base) $ conda activate ct

Afterward, Cell Typist can be installed from PyPi

(ct) $ pip install hcr-cell-typist

This will also install Jupyter, so after installation and activation of the ct environment, a jupyter session can be started with

(ct) $ jupyter notebook

Usage

An example workflow for analysis, covering all the API, can be found here.

We also provide a notebook covering merging of results and custom plotting.

Versions

A changelog with bug fixes and features per version can be found here