morphomapping 0.0.8

Analyze ImageStream Data

MorphoMapping

MorphoMapping is an analytical framework designed for the analysis of Imaging Flow Cytometry (IFC) data. It is based on our Python package, morphomapping, which provides tools for dimensionality reduction and clustering of IFC data. Step 2 and Step 4 can be considered optional.

Description

workflow	details
Step 1	IFC Data Acquisation
Step 2	Convert .daf to .FCS (R)
Step 3	morphomapping (Python)
Step 4	Cluster Analysis (R)

Getting started

Please refer to the documentation.

Installation

It is recommended to choose conda as your package manager. Conda can be obtained, e.g., by installing the Miniconda distribution. For detailed instructions, please refer to the respective documentation.

With conda installed, open your terminal and create a new environment by executing the following commands::

conda create -n morphomapping python=3.10
conda activate morphomapping

PyPI

Install morphomapping via the pypi release:

pip install morphomapping

Development Version

In order to get the latest version, install from GitHub using

pip install git+https://github.com/Wguido/MorphoMapping@main

Alternatively, clone the repository to your local hard drive via

git clone https://github.com/Wguido/MorphoMapping.git && cd MorphoMapping
git checkout --track origin/main
pip install .

Note that while MorphoMapping is in beta phase, you need to have access to the private repo.

Jupyter notebooks

Jupyter notebooks are highly recommended due to their extensive visualization capabilities. Install jupyter via

conda install jupyter

and run the notebook by entering jupyter-notebook into the terminal.

Dependencies

• The following Python packages are needed for MorphoMapping:

Package
bokeh
flowkit
hdbscan
matplotlib
numpy
openpyxl
pandas
scikit-learn
umap-learn

• The following R libraries (R V.4.2.1) are required for MorphoMapping's optional DAFtoFCS-Converter and the Cluster Analysis:

Library	Version
ggplot2	3.4.4
ggpubr	0.6.0
here	1.0.1
IFC	0.2.1
rstatix	0.7.2