Subcellular Chemical Imaging: New Avenues in Cell Biology

Decelle, Johan; Veronesi, Giulia; Gallet, Benoît; Stryhanyuk, Hryhoriy; Benettoni, Pietro; Schmidt, Matthias; Tucoulou, R.; Passarelli, Melissa K.; Bohic, Sylvain; Clode, Peta L.; Musat, Niculina

doi:10.1016/j.tcb.2019.12.007

Cited by 66 publications

(61 citation statements)

References 85 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Our observation of different intermediates of biomineralisation, a fundamental biogeochemical process that initiates carbon deposition in the oceans is another nice example. The major challenges in the future will be to correlate this approach with cryo-electron tomography in order to improve the resolution of specific subcellular structures to the molecular level, and to combine it with chemical imaging (Decelle et al, 2020) and fluorescence measurements with fluorophores/antibodies, in order to allow correlative microscopic studies on phytoplankton (Sartori et al, 2007;Stephens and Allan, 2003).…”

Section: Discussionmentioning

confidence: 99%

In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy

Uwizeye

Decelle

Jouneau

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Phytoplankton is a minor fraction of the global biomass playing a major role in primary production and climate. Despite improved understanding of phytoplankton diversity and genomics, we lack nanoscale subcellular imaging approaches to understand their physiology and cell biology. Here, we present a complete Focused Ion Beam -Scanning Electron Microscopy (FIB-SEM) workflow (from sample preparation to image processing) to generate nanometric 3D phytoplankton models. Tomograms of entire cells, representatives of six ecologically-successful phytoplankton unicellular eukaryotes, were used for quantitative morphometric analysis. Besides lineage-specific cellular architectures, we observed common features related to cellular energy management: i) conserved cell-volume fractions occupied by the different organelles; ii) consistent plastid-mitochondria interactions, iii) constant volumetric ratios in these energy-producing organelles. We revealed detailed subcellular features related to chromatin organization and to biomineralization. Overall, this approach opens new perspectives to study phytoplankton acclimation responses to abiotic and biotic factors at a relevant biological scale.

show abstract

Section: Discussionmentioning

confidence: 99%

In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy

Uwizeye

Decelle

Jouneau

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…In a broad sense, correlative microscopy refers to any combination of microscopy techniques (Karreman et al, 2016), microscopic X-ray computed tomography of excised tissue (Karreman et al, 2017), transmission electron microscopy (TEM) (Fuest et al, 2018), atmospheric or environmental scanning electron microscopy (SEM) (Peckys and de Jonge, 2015;Sato et al, 2019), cathodoluminescence of nanoparticles in SEM (Glenn et al, 2012), cryo-electron tomography (Tao et al, 2018), array tomography of electron microscopy (Burel et al, 2018;Collman et al, 2015;Micheva and Smith, 2007), X-ray holography, X-ray scanning diffraction (Bernhardt et al, 2018), X-ray fluorescence imaging and mass spectrometry imaging (Decelle et al, 2020). Some authors emphasized this integration of information from multiple imaging methods, by proposing a "morphomics" notation (Lucocq et al, 2015).…”

Section: Correlative Microscopymentioning

confidence: 99%

Correlating cell function and morphology by performing fluorescent immunocytochemical staining on the light-microscope stage

Kawano

Kakazu

Iwabuchi

et al. 2020

Preprint

View full text Add to dashboard Cite

ABSTRACTBackgroundCorrelation of fluorescence signals from functional changes in live cells with those from immunocytochemical indicators of their morphology following chemical fixation can be highly informative with regard to function-structure relationship. Such analyses can be technically challenging because they need consistently aligning the images between imaging sessions. Existing solutions include introducing artificial spatial landmarks and modifying the microscopes. However, these methods can require extensive changes to the experimental systems.New methodHere we introduce a simple approach for aligning images. It is based on two procedures: performing immunocytochemistry while a specimen stays on a microscope stage (on-stage), and aligning images using biological structures as landmarks after they are observed with transmitted-light optics in combination with fluorescence-filter sets.ResultsWe imaged a transient functional signal from a fluorescent Ca2+ indicator, and mapped it to neurites based on immunocytochemical staining of a structural marker. In the same preparation, we could identify presynaptically silent synapses, based on a lack of labeling with an indicator for synaptic vesicle recycling and on positive immunocytochemical staining for a structural marker of nerve terminals. On-stage immunocytochemistry minimized lateral translations and eliminated rotations, and transmitted-light images of neurites were sufficiently clear to enable spatial registration, effective at a single-pixel level.Comparison with existing methodsThis method aligned images with minimal change or investment in the experimental systems.ConclusionsThis method facilitates information retrieval across multiple imaging sessions, even when functional signals are transient or local, and when fluorescent signals in multiple imaging sessions do not match spatially.

show abstract

“…A recent review on subcellular chemical imaging using correlative workflows is given in Decelle et al . (2020).…”

Section: Introductionmentioning

confidence: 99%

Correlia: an ImageJ plug‐in to co‐register and visualise multimodal correlative micrographs

Rohde

Braumann

Schmidt

2020

Journal of Microscopy

Self Cite

View full text Add to dashboard Cite

Summary The correlation of different microscopic imaging techniques alongside with microanalytical methods is crucial to better understand biological processes on a subcellular level. For that, micrographs and chemical maps exhibiting both, very different spatial resolution and field‐of‐view but also a highly multimodal content has to be co‐registered. We developed the ImageJ/Fiji plug‐in Correlia that provides an environment for handling multimodal correlative microscopy data. Several linear and nonlinear registration methods using either feature or area‐based similarity measures can flexibly be cascaded to align and warp 2D microscopy data sets. The registration of data sets containing light‐ and electron micrographs as well as chemical maps acquired by secondary‐ion mass spectroscopy and energy‐dispersive X‐ray spectroscopy is demonstrated. Correlia is an open‐source tool developed particularly for the registration and analysis of highly multimodal 2D correlative microscopy data. Lay Description If a microscopic object is imaged correlatively by two or more different microscopes the acquired micrographs will have to be overlaid accurately using an image‐registration software. In cases of relatively similar image content creating such an overlay is straight‐forward but what if the fields‐of‐view and resolutions of the micrographs differ significantly? What if there are distortions in a micrograph which have to be corrected before creating an overlay? What if furthermore a chemical map shall be overlaid that merely shows regions in which a certain chemical element is present? The rapidly increasing number of applications in correlative microscopy is calling for an easy‐to‐use and flexible image registration software that can deal with these challenges. Having that in mind, we developed Correlia, an ImageJ/Fiji plug‐in that provides an environment for handling multimodal 2D correlative microscopy data‐sets. It allows for creating overlays using different registration algorithms that can flexibly be cascaded. In this paper we describe what is happening ‘under the hood’ and give two example data‐sets from microbiology which were registered using Correlia. Correlia is open source software and available from http://www.ufz.de/correlia ‐ including introductory examples, as the authors would like to encourage other scientists to process their individual correlative microscopy data using Correlia.

show abstract

Subcellular Chemical Imaging: New Avenues in Cell Biology

Cited by 66 publications

References 85 publications

In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy

In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy

Correlating cell function and morphology by performing fluorescent immunocytochemical staining on the light-microscope stage

Correlia: an ImageJ plug‐in to co‐register and visualise multimodal correlative micrographs

Contact Info

Product

Resources

About