Detecting and correcting false transients in calcium imaging

Jeffrey L. Gauthier, Sue Ann Koay, Edward H. Nieh, David W. Tank, Jonathan W. Pillow, Adam S. Charles

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


Population recordings of calcium activity are a major source of insight into neural function. Large datasets require automated processing, but this can introduce errors that are difficult to detect. Here we show that popular time course-estimation algorithms often contain substantial misattribution errors affecting 10–20% of transients. Misattribution, in which fluorescence is ascribed to the wrong cell, arises when overlapping cells and processes are imperfectly defined or not identified. To diagnose misattribution, we develop metrics and visualization tools for evaluating large datasets. To correct time courses, we introduce a robust estimator that explicitly accounts for contaminating signals. In one hippocampal dataset, removing contamination reduced the number of place cells by 15%, and 19% of place fields shifted by over 10 cm. Our methods are compatible with other cell-finding techniques, empowering users to diagnose and correct a potentially widespread problem that could alter scientific conclusions.

Original languageEnglish (US)
Pages (from-to)470-478
Number of pages9
JournalNature Methods
Issue number4
StatePublished - Apr 2022

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Biochemistry
  • Biotechnology
  • Cell Biology


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