Cell Analysis Tools

This library was developed for the Skala Lab at the Morgridge Institute for Reserach / University of Wisconsin-Madison to simplify single cell analysis of images. It contains many relevant functions used for pre-processing, processing analyzing, loading and summarizing images.

Single cell feature extraction code and example

  • The included single cell feature extraction example can be modified to

    • Load your fluorescence images and masks

    • Visualize sets of images

    • Extract features by iterating over very single region of interest

    • Finally aggregate features into a single CSV file for further data analysis

regionprops workflow example

Feature reduction example

  • PCA

PCA example

Dimensionality reduction example

  • t-SNE

tsne of example data

  • UMAP

umap of example data

Basic phasor plotting functions

  • Functions for transforming a lifetime decay into a phasor plot are included in the flim namespace

basic phasor plotting

Image Processing

  • Removing Noise –>

Dependencies

  • numpy

  • tifffile

  • pathlib

  • read_roi

  • os

  • matplotlib

  • re

  • skimage

  • pandas

Installation

Available through pip

pip install cell-analysis-tools

You could also clone the repository and install it manually by * changing directories to the cloned repo directory

pip install -e .

Examples

This library also contains examples scripts for various single cell analysis tasks:

  • Extracting features from fluorescence lifetime images

  • RandomForest, Logistic Regression and Support Vector Machine classification

  • Generating UMAPs

Examples On Gihub

Cite

Contents:

Indices and tables