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SCIP: a single-cell image processor toolbox.

Leonardo Martins1,2, Ramakanth Neeli-Venkata1, Samuel M D Oliveira1

  • 1Faculty of Biomedical Sciences and Engineering and Laboratory of Biosystem Dynamics of the BioMediTech Institute, Tampere University of Technology, Tampere, Finland.

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Summary

SCIP software analyzes time-lapse microscopy images of individual cells to understand cellular processes. This tool aids in discovering relationships between gene expression and cell division in various cell types.

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Area of Science:

  • Cell biology
  • Microscopy
  • Bioinformatics

Background:

  • Individual cells exhibit unique phenotypes influenced by internal and external factors.
  • Characterizing cellular dynamics requires observing multiple cells over time from various perspectives.
  • Identifying commonalities and variability in cellular processes is crucial for understanding cell behavior.

Purpose of the Study:

  • To introduce SCIP, a novel software for analyzing multi-modal, time-lapse microscopy images.
  • To enable detailed characterization of cellular morphology and function in individual cells and lineages.
  • To facilitate the study of relationships between diverse cellular processes.

Main Methods:

  • Development of SCIP software for automated and manual cell/lineage segmentation.
  • Implementation of automatic alignment for different microscopy channels.
  • Capability to detect, count, and characterize various intracellular components (e.g., fluorescent spots, nucleoids, Z rings).

Main Results:

  • SCIP successfully analyzes morphological and functional data from time-lapse microscopy.
  • The software allows for the detection and characterization of numerous cellular features and structures.
  • Exportable results in *mat files enable joint analysis of individual features and processes.

Conclusions:

  • SCIP provides a comprehensive platform for analyzing single-cell dynamics and lineage progression.
  • The software is applicable to various cell types, including prokaryotes and eukaryotes.
  • SCIP is expected to advance the understanding of relationships between small-scale (gene expression) and large-scale (cell division) cellular processes.