When light meets biology – how the specimen affects quantitative microscopy

Reiche, Michael; Aaron, Jesse; Boehm, Ulrike; DeSantis, Michael C.; Hobson, Chad M.; Khuon, Satya; Lee, Rachel; Chew, Teng‐Leong

doi:10.1242/jcs.259656

Cited by 14 publications

(10 citation statements)

References 158 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Absolute volume measurements are not possible from immunofluorescent material. Thus, relative comparisons between specimens require strictly comparable specimen processing, image acquisition, and image analysis [ 40 , 41 ]. Sufficient material from quiet-aged gerbils in particular was only available to us over prolonged periods of time.…”

Section: Resultsmentioning

confidence: 99%

Cochlear Ribbon Synapses in Aged Gerbils

Bovee,

Klump,

Pyott

et al. 2024

IJMS

View full text Add to dashboard Cite

In mammalian hearing, type-I afferent auditory nerve fibers comprise the basis of the afferent auditory pathway. They are connected to inner hair cells of the cochlea via specialized ribbon synapses. Auditory nerve fibers of different physiological types differ subtly in their synaptic location and morphology. Low-spontaneous-rate auditory nerve fibers typically connect on the modiolar side of the inner hair cell, while high-spontaneous-rate fibers are typically found on the pillar side. In aging and noise-damaged ears, this fine-tuned balance between auditory nerve fiber populations can be disrupted and the functional consequences are currently unclear. Here, using immunofluorescent labeling of presynaptic ribbons and postsynaptic glutamate receptor patches, we investigated changes in synaptic morphology at three different tonotopic locations along the cochlea of aging gerbils compared to those of young adults. Quiet-aged gerbils showed about 20% loss of afferent ribbon synapses. While the loss was random at apical, low-frequency cochlear locations, at the basal, high-frequency location it almost exclusively affected the modiolar-located synapses. The subtle differences in volumes of pre- and postsynaptic elements located on the inner hair cell’s modiolar versus pillar side were unaffected by age. This is consistent with known physiology and suggests a predominant, age-related loss in the low-spontaneous-rate auditory nerve population in the cochlear base, but not the apex.

show abstract

Section: Resultsmentioning

confidence: 99%

Cochlear Ribbon Synapses in Aged Gerbils

Bovee,

Klump,

Pyott

et al. 2024

IJMS

View full text Add to dashboard Cite

show abstract

“…Problems are averted if the core facility is consulted upfront, which oftentimes does not happen, either because users underestimate the complexity of the techniques and the hurdles to be taken to generate reliable results 23 or simply because the core facility's capacity may be limited to devote enough attention and resources to the project 5 . Scientists with little bioimaging experience might insufficiently consider the consequences of the suboptimal choice of equipment, instrument settings and sources of bias 24,25 . These factors influence whether an image accurately represents the biological phenomenon and the necessary workload from image acquisition to publication‐ready results.…”

Section: Part I: the Bioimage Data Life Cyclementioning

confidence: 99%

A practical guide to bioimaging research data management in core facilities

Schmidt,

Boissonnet,

Dohle

et al. 2024

Journal of Microscopy

View full text Add to dashboard Cite

Bioimage data are generated in diverse research fields throughout the life and biomedical sciences. Its potential for advancing scientific progress via modern, data‐driven discovery approaches reaches beyond disciplinary borders. To fully exploit this potential, it is necessary to make bioimaging data, in general, multidimensional microscopy images and image series, FAIR, that is, findable, accessible, interoperable and reusable. These FAIR principles for research data management are now widely accepted in the scientific community and have been adopted by funding agencies, policymakers and publishers. To remain competitive and at the forefront of research, implementing the FAIR principles into daily routines is an essential but challenging task for researchers and research infrastructures. Imaging core facilities, well‐established providers of access to imaging equipment and expertise, are in an excellent position to lead this transformation in bioimaging research data management. They are positioned at the intersection of research groups, IT infrastructure providers, the institution´s administration, and microscope vendors. In the frame of German BioImaging – Society for Microscopy and Image Analysis (GerBI‐GMB), cross‐institutional working groups and third‐party funded projects were initiated in recent years to advance the bioimaging community's capability and capacity for FAIR bioimage data management. Here, we provide an imaging‐core‐facility‐centric perspective outlining the experience and current strategies in Germany to facilitate the practical adoption of the FAIR principles closely aligned with the international bioimaging community. We highlight which tools and services are ready to be implemented and what the future directions for FAIR bioimage data have to offer.

show abstract

“…Filming the impact of SARS-CoV-2 on an entire cellular system from early infection to death would greatly improve our understanding of infection sequences and dynamics, yet the efforts to obtain such knowledge are precluded by the limitations of live microscopy. The various types of fluorescence microscopy induce nonneglectable phototoxicity and molecular perturbations due to the use of chemical or genetic labeling [8][9][10][11][12][13] . This limits the capacity to observe multiple targets over hours-long periods, which is the time scale necessary to capture the cellular changes induced by SARS-CoV-2.…”

Section: Introductionmentioning

confidence: 99%

Dynamic label-free analysis of SARS-CoV-2 infection reveals virus-induced subcellular remodeling

Saunders,

Monel,

Cayet

et al. 2023

Preprint

View full text Add to dashboard Cite

SummaryAssessing the impact of SARS-CoV-2 on organelle dynamics allows a better understanding of the mechanisms of viral replication. We combine label-free holo-tomographic microscopy (HTM) with Artificial Intelligence (AI) to visualize and quantify the subcellular changes triggered by SARS-CoV-2 infection. We study the dynamics of shape, position and dry mass of nucleoli, nuclei, lipid droplets (LD) and mitochondria within hundreds of single cells from early infection to syncytia formation and death. SARS-CoV-2 infection enlarges nucleoli, perturbs LD, changes mitochondrial shape and dry mass, and separates LD from mitochondria. We then used Bayesian statistics on organelle dry mass states to define organelle cross-regulation (OCR) networks and report modifications of OCR that are triggered by infection and syncytia formation. Our work highlights the subcellular remodeling induced by SARS-CoV-2 infection and provides a new AI-enhanced, label-free methodology to study in real-time the dynamics of cell populations and their content.

show abstract

When light meets biology – how the specimen affects quantitative microscopy

Cited by 14 publications

References 158 publications

Cochlear Ribbon Synapses in Aged Gerbils

Cochlear Ribbon Synapses in Aged Gerbils

A practical guide to bioimaging research data management in core facilities

Dynamic label-free analysis of SARS-CoV-2 infection reveals virus-induced subcellular remodeling

Contact Info

Product

Resources

About