In situ X-ray assisted electron microscopy staining for large biological samples

  1. Sebastian Ströh
  2. Eric W Hammerschmith
  3. David W Tank
  4. H Sebastian Seung
  5. Adrian Andreas Wanner  Is a corresponding author
  1. Princeton University, United States
  2. Paul Scherrer Institute, Switzerland

Abstract

Electron microscopy of biological tissue has recently seen an unprecedented increase in imaging throughput moving the ultrastructural analysis of large tissue blocks such as whole brains into the realm of the feasible. However, homogeneous, high quality electron microscopy staining of large biological samples is still a major challenge. To date, assessing the staining quality in electron microscopy requires running a sample through the entire staining protocol end-to-end, which can take weeks or even months for large samples, rendering protocol optimization for such samples to be inefficient. Here we present an in situ time-lapsed X-ray assisted staining procedure that opens the 'black box' of electron microscopy staining and allows observation of individual staining steps in real time. Using this novel method we measured the accumulation of heavy metals in large tissue samples immersed in different staining solutions. We show that the measured accumulation of osmium in fixed tissue obeys empirically a quadratic dependence between the incubation time and sample size. We found that potassium ferrocyanide, a classic reducing agent for osmium tetroxide, clears the tissue after osmium staining and that the tissue expands in osmium tetroxide solution, but shrinks in potassium ferrocyanide reduced osmium solution. X-ray assisted staining gave access to the in situ staining kinetics and allowed us to develop a diffusion-reaction-advection model that accurately simulates the measured accumulation of osmium in tissue. These are first steps towards in silico staining experiments and simulation-guided optimization of staining protocols for large samples. Hence, X-ray assisted staining will be a useful tool for the development of reliable staining procedures for large samples such as entire brains of mice, monkeys or humans.

Data availability

The code to analyze the X-ray projection images and to model the accumulation of heavy metals can be found on https://github.com/adwanner/XrayAssistedStaining. All X-ray data is available for download on https://www.ebi.ac.uk/empiar/ with dataset ID EMPIAR-10782.

Article and author information

Author details

  1. Sebastian Ströh

    Princeton Neuroscience Institute, Princeton University, Princeton, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8128-2617
  2. Eric W Hammerschmith

    Princeton Neuroscience Institute, Princeton University, Princeton, United States
    Competing interests
    No competing interests declared.
  3. David W Tank

    Princeton Neuroscience Institute, Princeton University, Princeton, United States
    Competing interests
    David W Tank, is an inventor of US Patent Application 16/681,028..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9423-4267
  4. H Sebastian Seung

    Princeton Neuroscience Institute, Princeton University, Princeton, United States
    Competing interests
    H Sebastian Seung, is an inventor of US Patent Application 16/681,028..
  5. Adrian Andreas Wanner

    Paul Scherrer Institute, Villigen, Switzerland
    For correspondence
    adrian.wanner@psi.ch
    Competing interests
    Adrian Andreas Wanner, is an inventor of US Patent Application 16/681,028..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5864-8577

Funding

CV Starr Fellowship in Neuroscience by the Princeton University

  • Adrian Andreas Wanner

National Institutes of Health (NS104648)

  • David W Tank
  • H Sebastian Seung

National Institutes of Health (1R01EY027036)

  • H Sebastian Seung

National Institutes of Health (U01NS090562)

  • H Sebastian Seung

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Andreas T Schaefer, The Francis Crick Institute, United Kingdom

Ethics

Animal experimentation: Animal use procedures were approved by the Princeton University Institutional Animal Care and Use Committee (protocol number 2000) and carried out in accordance with National Institutes of Health standards (AAALAC International Institutional Number: Unit #1001, PHS assurance ID D16-00273).

Version history

  1. Preprint posted: June 20, 2021 (view preprint)
  2. Received: July 13, 2021
  3. Accepted: October 18, 2022
  4. Accepted Manuscript published: October 20, 2022 (version 1)
  5. Version of Record published: November 15, 2022 (version 2)

Copyright

© 2022, Ströh et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 982
    views
  • 158
    downloads
  • 8
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Sebastian Ströh
  2. Eric W Hammerschmith
  3. David W Tank
  4. H Sebastian Seung
  5. Adrian Andreas Wanner
(2022)
In situ X-ray assisted electron microscopy staining for large biological samples
eLife 11:e72147.
https://doi.org/10.7554/eLife.72147

Share this article

https://doi.org/10.7554/eLife.72147

Further reading

    1. Genetics and Genomics
    2. Neuroscience
    Bohan Zhu, Richard I Ainsworth ... Javier González-Maeso
    Research Article

    Genome-wide association studies have revealed >270 loci associated with schizophrenia risk, yet these genetic factors do not seem to be sufficient to fully explain the molecular determinants behind this psychiatric condition. Epigenetic marks such as post-translational histone modifications remain largely plastic during development and adulthood, allowing a dynamic impact of environmental factors, including antipsychotic medications, on access to genes and regulatory elements. However, few studies so far have profiled cell-specific genome-wide histone modifications in postmortem brain samples from schizophrenia subjects, or the effect of antipsychotic treatment on such epigenetic marks. Here, we conducted ChIP-seq analyses focusing on histone marks indicative of active enhancers (H3K27ac) and active promoters (H3K4me3), alongside RNA-seq, using frontal cortex samples from antipsychotic-free (AF) and antipsychotic-treated (AT) individuals with schizophrenia, as well as individually matched controls (n=58). Schizophrenia subjects exhibited thousands of neuronal and non-neuronal epigenetic differences at regions that included several susceptibility genetic loci, such as NRG1, DISC1, and DRD3. By analyzing the AF and AT cohorts separately, we identified schizophrenia-associated alterations in specific transcription factors, their regulatees, and epigenomic and transcriptomic features that were reversed by antipsychotic treatment; as well as those that represented a consequence of antipsychotic medication rather than a hallmark of schizophrenia in postmortem human brain samples. Notably, we also found that the effect of age on epigenomic landscapes was more pronounced in frontal cortex of AT-schizophrenics, as compared to AF-schizophrenics and controls. Together, these data provide important evidence of epigenetic alterations in the frontal cortex of individuals with schizophrenia, and remark for the first time on the impact of age and antipsychotic treatment on chromatin organization.

    1. Neuroscience
    Aedan Yue Li, Natalia Ladyka-Wojcik ... Morgan Barense
    Research Article

    Combining information from multiple senses is essential to object recognition, core to the ability to learn concepts, make new inferences, and generalize across distinct entities. Yet how the mind combines sensory input into coherent crossmodal representations - the crossmodal binding problem - remains poorly understood. Here, we applied multi-echo fMRI across a four-day paradigm, in which participants learned 3-dimensional crossmodal representations created from well-characterized unimodal visual shape and sound features. Our novel paradigm decoupled the learned crossmodal object representations from their baseline unimodal shapes and sounds, thus allowing us to track the emergence of crossmodal object representations as they were learned by healthy adults. Critically, we found that two anterior temporal lobe structures - temporal pole and perirhinal cortex - differentiated learned from non-learned crossmodal objects, even when controlling for the unimodal features that composed those objects. These results provide evidence for integrated crossmodal object representations in the anterior temporal lobes that were different from the representations for the unimodal features. Furthermore, we found that perirhinal cortex representations were by default biased towards visual shape, but this initial visual bias was attenuated by crossmodal learning. Thus, crossmodal learning transformed perirhinal representations such that they were no longer predominantly grounded in the visual modality, which may be a mechanism by which object concepts gain their abstraction.