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Cells
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Combined and Correlated Microscopy for Structure-Function Biology
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Combined and Correlated Microscopy for Structure-Function Biology

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cellular Biophysics".

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 5489

Special Issue Editors

Prof. Dr. Marco Canossa

E-Mail Website
Guest Editor
Department of Cellular, Computational and Integrative Biology (CIBIO) University of Trento, 38123 Povo, Italy
Interests: mechanisms of neurotrophin plasticity; neuron-astrocyte interaction; neuronal polarity; mechanisms of adult neurogenesis; memory engrams
Dr. Spartaco Santi

E-Mail Website
Guest Editor
Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche (CNR), 40136 Bologna, Italy
Interests: extracellular vesicles; 3D spheroids; glial microdomains; super-resolution microscopy; deep imaging

Special Issue Information

Dear Colleagues,

Many essential biological questions in contemporary cellular biology are based on information obtained by the use of various microscopy techniques. While separate entities characterized by individual features, the use of multiple imaging approaches is increasingly more often viewed as deeply complementary. Technological innovations in imaging techniques, labeling tools and functional fluorescent probes have powered the development of a series of hybrid approaches, allowing correlating functional fluorescence microscopy data and ultrastructural information from a structure–function singular event. In this Special Issue, we aim to examine several currently available examples of hybrid microscopy attaining correlative approaches in light and electron microscopy, and discuss their potential and limitations with respect to structure–function applications.

Prof. Dr. Marco Canossa
Dr. Spartaco Santi
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cells is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (2 papers)

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Research

12 pages, 7528 KiB  
Communication
Structured Illumination Microscopy Improves Spot Detection Performance in Spatial Transcriptomics
by Alejandro Linares, Carlo Brighi, Sergio Espinola, Francesco Bacchi and Álvaro H. Crevenna
Cells 2023, 12(9), 1310; https://0-doi-org.brum.beds.ac.uk/10.3390/cells12091310 - 04 May 2023
Cited by 2 | Viewed by 2289
Abstract
Spatial biology is a rapidly growing research field that focuses on the transcriptomic or proteomic profiling of single cells within tissues with preserved spatial information. Imaging-based spatial transcriptomics uses epifluorescence microscopy, which has shown remarkable results for the identification of multiple targets in [...] Read more.
Spatial biology is a rapidly growing research field that focuses on the transcriptomic or proteomic profiling of single cells within tissues with preserved spatial information. Imaging-based spatial transcriptomics uses epifluorescence microscopy, which has shown remarkable results for the identification of multiple targets in situ. Nonetheless, the number of genes that can be reliably visualized is limited by the diffraction of light. Here, we investigate the effect of structured illumination (SIM), a super-resolution microscopy approach, on the performance of single-gene transcript detection in spatial transcriptomics experiments. We performed direct mRNA-targeted hybridization in situ sequencing for multiple genes in mouse coronal brain tissue sections. We evaluated spot detection performance in widefield and confocal images versus those with SIM in combination with 20×, 25× and 60× objectives. In general, SIM increases the detection efficiency of gene transcript spots compared to widefield and confocal modes. For each case, the specific fold increase in localizations is dependent on gene transcript density and the numerical aperture of the objective used, which has been shown to play an important role, especially for densely clustered spots. Taken together, our results suggest that SIM has the capacity to improve spot detection and overall data quality in spatial transcriptomics. Full article
(This article belongs to the Special Issue Combined and Correlated Microscopy for Structure-Function Biology)
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28 pages, 11766 KiB  
Article
Correlative Multi-Modal Microscopy: A Novel Pipeline for Optimizing Fluorescence Microscopy Resolutions in Biological Applications
by Simone Pelicci, Laura Furia, Pier Giuseppe Pelicci and Mario Faretta
Cells 2023, 12(3), 354; https://0-doi-org.brum.beds.ac.uk/10.3390/cells12030354 - 17 Jan 2023
Cited by 2 | Viewed by 2507
Abstract
The modern fluorescence microscope is the convergence point of technologies with different performances in terms of statistical sampling, number of simultaneously analyzed signals, and spatial resolution. However, the best results are usually obtained by maximizing only one of these parameters and finding a [...] Read more.
The modern fluorescence microscope is the convergence point of technologies with different performances in terms of statistical sampling, number of simultaneously analyzed signals, and spatial resolution. However, the best results are usually obtained by maximizing only one of these parameters and finding a compromise for the others, a limitation that can become particularly significant when applied to cell biology and that can reduce the spreading of novel optical microscopy tools among research laboratories. Super resolution microscopy and, in particular, molecular localization-based approaches provide a spatial resolution and a molecular localization precision able to explore the scale of macromolecular complexes in situ. However, its use is limited to restricted regions, and consequently few cells, and frequently no more than one or two parameters. Correlative microscopy, obtained by the fusion of different optical technologies, can consequently surpass this barrier by merging results from different spatial scales. We discuss here the use of an acquisition and analysis correlative microscopy pipeline to obtain high statistical sampling, high content, and maximum spatial resolution by combining widefield, confocal, and molecular localization microscopy. Full article
(This article belongs to the Special Issue Combined and Correlated Microscopy for Structure-Function Biology)
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