SpheroidPy 0.1.0

Python Package for the Spatial and Temporal Analysis of Spheroid Imaging Data

SpheroidPy

Overview

SpheroidPy is a Python package designed for the management and analysis of in-vitro spheroid data. It offers a framework to facilitate the handling, segmentation, and analysis of extensive collections of spheroid microscopy images. Furthermore, it enables users to extract spatial and temporal features gaining insights into the dynamics of underlying biological processes. While primarily developed and optimized for cancer spheroid proliferation and cytotoxicity assays, it can be adapted to other cell entities and three-dimensional assay systems.

Applications

Proliferation Assays

Proliferation assays are essential for studying growth kinetics in three-dimensional spheroid cultures. Besides simple growth curves, more complex behaviors - such as the emergence of a necrotic core at a critical radius $R_c$ or saturation at large sizes - can be assessed from such data. SpheroidPy facilitates data import, spheroid segmentation, and comprehensive analysis of growth dynamics, including automated statistical evaluations.

Prerequisits

To ensure a clean and reproducible setup, we recommend installing the package inside a dedicated Conda environment. Begin by installing Anaconda, then create and activate a new environment using the commands below. This can be done in a Anaconda Prompt (Windows) or Terminal (Mac/Linux) and guarantees that all dependencies—including optional deep-learning frameworks—are isolated from your system installation.

conda create -n spheroidpy python=3.10
conda activate spheroid

Optionally, Jupyter Notebook can be installed if not already available:

conda install jupyter

Installation

Using PyPI

SpheroidPy is available on PyPI and can be installed using the following command

pip install SpheroidPy

From Source

Alternatively, the package can be installed directly from source. Therefore, the repository has to be downloaded. After navigating to the folder containing package, it can be installed using

cd path/to/SpheroidPy             # navigate to the parent folder
pip install .                     # install the package

Usage

After installation, SpheroidPy can be used to analyze spheroid microscopy data following a hierarchical workflow from single images to full experiments.

At the core, individual microscopy images are represented by SpheroidImage objects, which provide functionality for segmentation and feature extraction:

from SpheroidPy.spheroid import SpheroidImage

spheroid = SpheroidImage(
    brightfield='path/to/image.tif',
    image_size=(1700, 1270)
)

spheroid.segmentation()
radius = spheroid.radius

Time-resolved measurements of the same spheroid can be organized in a SpheroidSeries, enabling the analysis of temporal dynamics:

from SpheroidPy.spheroid import SpheroidSeries

series = SpheroidSeries("Example")
series.add_spheroid_image(spheroid, timestamp)
series.segmentation()

series.metric('radius', plot=True)

Multiple series (e.g., technical replicates) can be combined in a SpheroidCollection for statistical evaluation:

from SpheroidPy.spheroid import SpheroidCollection

collection = SpheroidCollection("Collection", [series])
collection.metric('radius', mean=True)

For structured comparison across experimental conditions, collections can be grouped in a Result:

from SpheroidPy.experiment import Result

result = Result("Experiment", condition="concentration")
result.add_collection(collection, condition=0)

At the highest level, complete workflows can be organized and persisted using the Experiment class:

from SpheroidPy import Experiment

experiment = Experiment(name="MyExperiment", path="path/to/project")

For high-throughput live-cell imaging experiments, dedicated LiveCellReplicate and Platemap classes enable structured handling of microwell plate layouts, automated image assignment, and condition-based grouping of wells:

replicate = result.replicate('Replicate1', layout=96)
replicate.platemap.cell_line('CellLineA', {'B2:G3':0, 'B4:G5':10})

replicate.load_images('path/to/data', ['PhaseContrast'], ['green'], ['red'],
                      image_size=(1700,1270))

Overall, SpheroidPy enables a consistent transition from single-image analysis to large-scale, reproducible experiments within a unified framework.