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Cells
Special Issues
Imaging Methods in Cell Biology
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Imaging Methods in Cell Biology

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

Deadline for manuscript submissions: 31 July 2025 | Viewed by 5664

Special Issue Editors

Prof. Claudia Moscheni

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Guest Editor
Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, Milan, Italy
Interests: mitochondria; autophagy; extracellular matrix; electron microscopy
Special Issues, Collections and Topics in MDPI journals
Prof. Nicoletta Gagliano

E-Mail Website
Guest Editor
Department of Biomedical Sciences for Health, Università degli Studi di Milano, 20133 Milan, Italy
Interests: collagen turnover; extracellular matrix remodeling; epithelial-to-mesenchymal transition; fibrosis; tendon biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As early as the 17th century, Galileo considered imaging as “the eyes of science”. Nowadays, several imaging techniques provide researchers with a wealth of specific and quantitative imaging information about molecules and cells, and their continuous development and improvement are crucial in disseminating new knowledge in various fields of life sciences. New imaging methods and instrumentation have improved resolution, signal detection, data collection, and manipulation for each sample type, enabling the visualization of a wide range multidimensional and multiparametric data.

The combination of whole-slide imaging at single-cell resolution in spatial biology studies allows for the visualization and quantitative analysis of biomarker expression and co-expression, and multiplexed methods increase the number of disease-specific biomarkers that can be detected simultaneously.

This allows for the dynamic knowledge of biological system components and their respective cellular processes, bridging the gap between morphological and molecular approaches, and can provide a potent tool to diagnose patients, establish the efficacy of therapeutic treatments, and monitor the recurrence of disease. Indeed, the ever-increasing diffusion and precision of imaging tools and the increasingly in-depth knowledge of biological processes allow the development of systems biology models that aim to have real predictive capabilities.

The purpose of this Special Issue is to shed light on the recent advances and development of imaging methods and approaches in different fields of cell biology research.

Prof. Claudia Moscheni
Prof. Nicoletta Gagliano
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.

Keywords

  • cellular organelles
  • molecular function
  • molecular interaction
  • disease- and drug-related subcellular phenomena
  • single-molecule imaging
  • light microscopy
  • electron microscopy
  • fluorescence microscopy
  • fluorescence correlation methods
  • fluorescence lifetime imaging microscopy (FLIM)
  • Raman microscopy
  • spatial biology

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

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Research

29 pages, 5579 KiB  
Article
Simulation and Quantitative Analysis of Spatial Centromere Distribution Patterns
by Adib Keikhosravi, Krishnendu Guin, Gianluca Pegoraro and Tom Misteli
Cells 2025, 14(7), 491; https://doi.org/10.3390/cells14070491 - 25 Mar 2025
Viewed by 360
Abstract
A prominent feature of eukaryotic chromosomes are centromeres, which are specialized regions of repetitive DNA required for faithful chromosome segregation during cell division. In interphase cells, centromeres are non-randomly positioned in the three-dimensional space of the nucleus in a cell type-specific manner. The [...] Read more.
A prominent feature of eukaryotic chromosomes are centromeres, which are specialized regions of repetitive DNA required for faithful chromosome segregation during cell division. In interphase cells, centromeres are non-randomly positioned in the three-dimensional space of the nucleus in a cell type-specific manner. The functional relevance and the cellular mechanisms underlying this localization are unknown, and quantitative methods to measure distribution patterns of centromeres in 3D space are needed. Here, we developed an analytical framework that combines sensitive clustering metrics and advanced modeling techniques for the quantitative analysis of centromere distributions at the single-cell level. To identify a robust quantitative measure for centromere clustering, we benchmarked six metrics for their ability to sensitively detect changes in centromere distribution patterns from high-throughput imaging data of human cells, both under normal conditions and upon experimental perturbation of centromere distribution. We found that Ripley’s K function has the highest accuracy with minimal sensitivity to variations in the number of centromeres, making it the most suitable metric for measuring centromere distributions. As a complementary approach, we also developed and validated spatial models to replicate centromere distribution patterns, and we show that a radially shifted Gaussian distribution best represents the centromere patterns seen in human cells. Our approach creates tools for the quantitative characterization of spatial centromere distributions with applications in both targeted studies of centromere organization and unbiased screening approaches. Full article
(This article belongs to the Special Issue Imaging Methods in Cell Biology)
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19 pages, 4876 KiB  
Article
Systematic Comparison of FBS and Medium Variation Effect on Key Cellular Processes Using Morphological Profiling
by Timofey Lebedev, Alesya Mikheeva, Valentina Gasca, Pavel Spirin and Vladimir Prassolov
Cells 2025, 14(5), 336; https://doi.org/10.3390/cells14050336 - 25 Feb 2025
Viewed by 986
Abstract
Although every cell biologist knows the importance of selecting the right growth conditions and it is well known that the composition of growth medium may vary depending on a product brand or lot affecting many cellular processes, still those effects are poorly systematized. [...] Read more.
Although every cell biologist knows the importance of selecting the right growth conditions and it is well known that the composition of growth medium may vary depending on a product brand or lot affecting many cellular processes, still those effects are poorly systematized. We addressed this issue by comparing the effect of 12 fetal bovine sera (FBS) and eight growth media from different brands on the morphological and functional parameters of five cell types: lung adenocarcinoma, neuroblastoma, glioblastoma, embryonic kidney, and colorectal cancer cells. Using high-throughput imaging, we compared cell proliferation; performed morphological profiling based on the imaging of 561,519 cells; measured extracellular regulated kinases (ERK1/2) activity, mitochondria potential, and lysosome accumulation; and compared cell sensitivity to drugs, response to EGF stimulation, and ability to differentiate. We found that changes in cell proliferation and morphology were independent, and morphological changes were associated with differences in mitochondria potential or the cell’s ability to differentiate. Surprisingly, the most drastic differences were detected in serum-free conditions, where medium choice affected cell survival and response to EGF. Overall, our data may be used to improve the reproducibility of experiments involving cell cultures, and the effects of 28 growth conditions on proliferation and 44 morphological parameters can be explored through a Shinyapp. Full article
(This article belongs to the Special Issue Imaging Methods in Cell Biology)
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18 pages, 14876 KiB  
Article
Three-Dimensional Cell Culture Micro-CT Visualization within Collagen Scaffolds in an Aqueous Environment
by Sergey Tkachev, Natalia Chepelova, Gevorg Galechyan, Boris Ershov, Danila Golub, Elena Popova, Artem Antoshin, Aliia Giliazova, Sergei Voloshin, Yuri Efremov, Elena Istranova and Peter Timashev
Cells 2024, 13(15), 1234; https://doi.org/10.3390/cells13151234 - 23 Jul 2024
Cited by 1 | Viewed by 3756
Abstract
Among all of the materials used in tissue engineering in order to develop bioequivalents, collagen shows to be the most promising due to its superb biocompatibility and biodegradability, thus becoming one of the most widely used materials for scaffold production. However, current imaging [...] Read more.
Among all of the materials used in tissue engineering in order to develop bioequivalents, collagen shows to be the most promising due to its superb biocompatibility and biodegradability, thus becoming one of the most widely used materials for scaffold production. However, current imaging techniques of the cells within collagen scaffolds have several limitations, which lead to an urgent need for novel methods of visualization. In this work, we have obtained groups of collagen scaffolds and selected the contrasting agents in order to study pores and patterns of cell growth in a non-disruptive manner via X-ray computed microtomography (micro-CT). After the comparison of multiple contrast agents, a 3% aqueous phosphotungstic acid solution in distilled water was identified as the most effective amongst the media, requiring 24 h of incubation. The differences in intensity values between collagen fibers, pores, and masses of cells allow for the accurate segmentation needed for further analysis. Moreover, the presented protocol allows visualization of porous collagen scaffolds under aqueous conditions, which is crucial for the multimodal study of the native structure of samples. Full article
(This article belongs to the Special Issue Imaging Methods in Cell Biology)
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