PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies

Grzegorz Bokota,Jacek Sroka,Adriana Magalska,Nirmal Das,Agnieszka Grabowska,Subhadip Basu,Yana Yushkevich,Dariusz Plewczynski,Pawel Trzaskoma

doi:10.1186/s12859-021-03984-1

Abstract

BackgroundBioimaging techniques offer a robust tool for studying molecular pathways and morphological phenotypes of cell populations subjected to various conditions. As modern high-resolution 3D microscopy provides access to an ever-increasing amount of high-quality images, there arises a need for their analysis in an automated, unbiased, and simple way. Segmentation of structures within the cell nucleus, which is the focus of this paper, presents a new layer of complexity in the form of dense packing and significant signal overlap. At the same time, the available segmentation tools provide a steep learning curve for new users with a limited technical background. This is especially apparent in the bulk processing of image sets, which requires the use of some form of programming notation.ResultsIn this paper, we present PartSeg, a tool for segmentation and reconstruction of 3D microscopy images, optimised for the study of the cell nucleus. PartSeg integrates refined versions of several state-of-the-art algorithms, including a new multi-scale approach for segmentation and quantitative analysis of 3D microscopy images. The features and user-friendly interface of PartSeg were carefully planned with biologists in mind, based on analysis of multiple use cases and difficulties encountered with other tools, to offer an ergonomic interface with a minimal entry barrier. Bulk processing in an ad-hoc manner is possible without the need for programmer support. As the size of datasets of interest grows, such bulk processing solutions become essential for proper statistical analysis of results. Advanced users can use PartSeg components as a library within Python data processing and visualisation pipelines, for example within Jupyter notebooks. The tool is extensible so that new functionality and algorithms can be added by the use of plugins. For biologists, the utility of PartSeg is presented in several scenarios, showing the quantitative analysis of nuclear structures.ConclusionsIn this paper, we have presented PartSeg which is a tool for precise and verifiable segmentation and reconstruction of 3D microscopy images. PartSeg is optimised for cell nucleus analysis and offers multi-scale segmentation algorithms best-suited for this task. PartSeg can also be used for the bulk processing of multiple images and its components can be reused in other systems or computational experiments.

Highlights

For a decade, high-throughput bioimaging techniques offered a robust tool for studying molecular pathways and morphological phenotypes of cell populations subjected to various conditions [1, 2]
The Chromosome Conformation Capture-method of chromatin interaction study (3-C) based methods, which decipher folding of chromatin, quantify the probability of interaction between two genomic fragments, such as promoters and enhancers, that are in close spatial proximity, but may be dispersed far across the genome
We provide two tutorials, which show how to use PartSeg from the biologist’s perspective with the Graphical User Interface (GUI) and from the bioinformatician’s perspective as a library

Summary

Introduction

Bioimaging techniques offer a robust tool for studying molecular pathways and morphological phenotypes of cell populations subjected to various conditions. The available segmentation tools provide a steep learning curve for new users with a limited technical background. This is especially apparent in the bulk processing of image sets, which requires the use of some form of programming notation. The 3-C based methods, which decipher folding of chromatin, quantify the probability of interaction between two genomic fragments, such as promoters and enhancers, that are in close spatial proximity, but may be dispersed far across the genome To refine this biochemical data, showing the outcome averaged over millions of cells, precise microscopic analysis of nuclear components like genes, chromatin, and nuclear domains is necessary. Microscopy is often used for verification, at scales of individual cells or even genetic copies

Results

Discussion

Conclusion