SpotMAX: a generalist framework for multi-dimensional automatic spot detection and quantification

  1. Francesco Padovani
  2. Ivana Čavka
  3. Ana Rita Rodrigues Neves
  4. Cristina Piñeiro López
  5. Nada Al-Refaie
  6. Leonardo Bolcato
  7. Dimitra Chatzitheodoridou
  8. Yagya Chadha
  9. Xiaofeng A. Su
  10. Jette Lengefeld
  11. Daphne S. Cabianca
  12. Simone Köhler
  13. Kurt M. Schmoller

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Abstract

The analysis of spot-like structures is a widespread task in microscopy-based cell biology. Existing solutions are typically specific to single applications and do not use multi-dimensional information from 5D datasets. Therefore, experimental scientists often resort to subjective manual annotation. Here, we present SpotMAX, a generalist AI-driven framework for automated spot detection and quantification. SpotMAX leverages the full scope of multi-dimensional datasets with an easy-to-use interface and an embedded framework for cell segmentation and tracking. SpotMAX outperforms state-of-the-art tools, and in some cases, even expert human annotators. We applied SpotMAX across diverse experimental questions, ranging from meiotic crossover events in C. elegans to mitochondrial DNA dynamics in S. cerevisiae and telomere length in mouse stem cells, leading to new biological insights. With its flexibility in integrating AI workflows, we anticipate that SpotMAX will become the standard for spot analysis in microscopy data.

Source code: https://github.com/SchmollerLab/SpotMAX

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  1. Arcadia Science

    revealed an unexpected mechanism that selectively targets nuclei282with errors in crossover regulation for apoptosis independently of the DNA damage checkpoint

    Is it known that the presence of RAD-51 foci alone is a reliable proxy for the activation of the DNA damage checkpoint in late meiotic prophase? (I'm not sure, but I wouldn't be surprised if it is not)

  2. Arcadia Science

    SpotMAX performs local peak detection with a footprint determined from the expected spot size

    Does SpotMAX support a range of expected spot sizes, or does it require one specific size?

  3. Arcadia Science

    Crucially, we provide an intuitive and user-friendly GUI integrated into the Cell-ACDC software9

    I think it'd be helpful to briefly explain what Cell-ACDC is and why it is important that SpotMAX is integrated into it, as some readers may not be familiar with it.

  4. Arcadia Science

    The ground truth in this dataset is known a priori215because there are 6 chromosomal crossovers in almost every cel

    I don't think it's quite accurate to say that the ground truth is known here unless the meaning of "in almost every cell" can be quantified. I agree that the fact that SpotMAX finds six foci in 97% of nuclei is qualitatively consistent with the biology of COSA-1 foci, but there's no way to quantify this performance without first quantifying the true prevalence of nuclei with more or less than six foci (and I think we do know it can't be 100%).

    It's also important to specify the meiotic stage (that is, the position of the nuclei within the gonad) at which foci are counted, since (if I recall correctly) COSA-1 foci appear gradually, so I think in mid-pachytene there will be many more nuclei with fewer than six foci than at late pachytene.

  5. Arcadia Science

    The representative images show two instances where the human made a counting218mistake

    If I recall correctly, COSA-1 foci aren't always diffraction-limited, so I'm not sure that it's really possible to determine the true number of foci in the two examples shown, at least from the 2D images shown in the figure (though I agree that the example on the left does look a lot like two barely-separated distinct foci)

  6. Version published to 10.1101/2024.10.22.619610v2 on bioRxiv
  7. Version published to 10.1101/2024.10.22.619610v1 on bioRxiv