AggreCount: an unbiased image analysis tool for identifying and quantifying cellular aggregates in a spatially defined manner

J Biol Chem. 2020 Dec 18;295(51):17672-17683. doi: 10.1074/jbc.RA120.015398.


Protein quality control is maintained by a number of integrated cellular pathways that monitor the folding and functionality of the cellular proteome. Defects in these pathways lead to the accumulation of misfolded or faulty proteins that may become insoluble and aggregate over time. Protein aggregates significantly contribute to the development of a number of human diseases such as amyotrophic lateral sclerosis, Huntington's disease, and Alzheimer's disease. In vitro, imaging-based, cellular studies have defined key biomolecular components that recognize and clear aggregates; however, no unifying method is available to quantify cellular aggregates, limiting our ability to reproducibly and accurately quantify these structures. Here we describe an ImageJ macro called AggreCount to identify and measure protein aggregates in cells. AggreCount is designed to be intuitive, easy to use, and customizable for different types of aggregates observed in cells. Minimal experience in coding is required to utilize the script. Based on a user-defined image, AggreCount will report a number of metrics: (i) total number of cellular aggregates, (ii) percentage of cells with aggregates, (iii) aggregates per cell, (iv) area of aggregates, and (v) localization of aggregates (cytosol, perinuclear, or nuclear). A data table of aggregate information on a per cell basis, as well as a summary table, is provided for further data analysis. We demonstrate the versatility of AggreCount by analyzing a number of different cellular aggregates including aggresomes, stress granules, and inclusion bodies caused by huntingtin polyglutamine expansion.

Keywords: Huntington disease; ImageJ; aggregate; aggregation; aggresome; amyotrophic lateral sclerosis (ALS) (Lou Gehrig disease); image-based analysis; inclusion body; microscopic imaging; misfolded protein; p97/valosin-containing protein; polyQ inclusion body; polyubiquitin chain; protein aggregation; protein misfolding p97/valosin-containing protein; protein quality control; proteostasis; stress granule; ubiquitin.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing / deficiency
  • Adaptor Proteins, Signal Transducing / genetics
  • Amyotrophic Lateral Sclerosis / metabolism
  • Amyotrophic Lateral Sclerosis / pathology
  • Arsenites / pharmacology
  • Cytoplasmic Granules / chemistry
  • Cytoplasmic Granules / drug effects
  • Fluorescent Dyes / chemistry
  • HeLa Cells
  • Humans
  • Huntington Disease / metabolism
  • Huntington Disease / pathology
  • Image Processing, Computer-Assisted
  • Inclusion Bodies / chemistry
  • Microscopy, Fluorescence / methods*
  • Protein Aggregates* / drug effects
  • Proteins / analysis*
  • Proteins / metabolism
  • Puromycin / pharmacology
  • Sodium Compounds / pharmacology


  • Adaptor Proteins, Signal Transducing
  • Arsenites
  • Fluorescent Dyes
  • Protein Aggregates
  • Proteins
  • Sodium Compounds
  • UBXN1 protein, human
  • sodium arsenite
  • Puromycin