Macro photography with Lighsheet Illumination Enables Whole Expanded Brain Imaging with Single-cell Resolution

Chia-Ming Lee;  ; Xuejiao Tian; Chieh Tsao; Peilin Chen; Tzyy-Nan Huang; Yi-Ping Hsueh; Bi-Chang Chen;  ;  ;  ;  ;  ;  ;  ;  ;

doi:10.15190/d.2021.12

Macro photography with Lighsheet Illumination Enables Whole Expanded Brain Imaging with Single-cell Resolution

Discoveries ◽

10.15190/d.2021.12 ◽

2021 ◽

Vol 9 (3) ◽

pp. e133

Author(s):

Chia-Ming Lee ◽

◽

Xuejiao Tian ◽

Chieh Tsao ◽

Peilin Chen ◽

...

Keyword(s):

Single Cell ◽

Brain Imaging ◽

Mouse Brain ◽

Structural Information ◽

Depth Of Field ◽

Direct Visualization ◽

Camera Lens ◽

Optical Magnification ◽

Organ Level ◽

Working Distance

Macro photography allows direct visualization of the enlarged whole mouse brain by a combination of lightsheet illumination and expansion microscopy with single-cell resolution. Taking advantage of the long working distance of a camera lens, we imaged a 3.7 cm thick, transparent, fluorescently-labeled expanded brain. In order to improve 3D sectioning capability, we used lightsheet excitation confined as the depth of field of the camera lens. Using 4x sample expansion and 5x optical magnification, macro photography enables imaging of expanded whole mouse brain with an effective resolution of 300 nm, which provides the subcellular structural information at the organ level.

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Direct visualization of phase-separated domains in lipid membranes

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100082315 ◽

1978 ◽

Vol 36 (2) ◽

pp. 290-291

Author(s):

S. W. Hui ◽

T. P. Stewart

Keyword(s):

Lipid Membranes ◽

Structural Information ◽

Freeze Fracture ◽

Biological Molecules ◽

Vacuum Drying ◽

Direct Visualization ◽

X Ray Diffraction ◽

Electron Microscopic ◽

X Ray ◽

Hydrocarbon Chains

Direct electron microscopic study of biological molecules has been hampered by such factors as radiation damage, lack of contrast and vacuum drying. In certain cases, however, the difficulties may be overcome by using redundent structural information from repeating units and by various specimen preservation methods. With bilayers of phospholipids in which both the solid and fluid phases co-exist, the ordering of the hydrocarbon chains may be utilized to form diffraction contrast images. Domains of different molecular packings may be recgnizable by placing properly chosen filters in the diffraction plane. These domains would correspond to those observed by freeze fracture, if certain distinctive undulating patterns are associated with certain molecular packing, as suggested by X-ray diffraction studies. By using an environmental stage, we were able to directly observe these domains in bilayers of mixed phospholipids at various temperatures at which their phases change from misible to inmissible states.

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Faculty Opinions recommendation of Single-cell mRNA isoform diversity in the mouse brain.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727274397.793532675 ◽

2017 ◽

Author(s):

Paul Pavlidis

Keyword(s):

Single Cell ◽

Mouse Brain ◽

Isoform Diversity ◽

Mrna Isoform

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Faculty Opinions recommendation of Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.732844079.793548900 ◽

2018 ◽

Author(s):

Yann Herault

Keyword(s):

Spinal Cord ◽

Single Cell ◽

Mouse Brain ◽

Single Cell Profiling ◽

Developing Mouse Brain ◽

Brain And Spinal Cord

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Induction and transmission of oncogene-induced senescence

Cellular and Molecular Life Sciences ◽

10.1007/s00018-020-03638-0 ◽

2020 ◽

Author(s):

Nattaphong Rattanavirotkul ◽

Kristina Kirschner ◽

Tamir Chandra

Keyword(s):

Stress Response ◽

Single Cell ◽

Cellular Stress ◽

Cellular Stress Response ◽

End Points ◽

Oncogene Activation ◽

Suppressor Mechanism ◽

Bona Fide ◽

Organ Level ◽

Complex Scenario

Abstract Senescence is a cellular stress response triggered by diverse stressors, including oncogene activation, where it serves as a bona-fide tumour suppressor mechanism. Senescence can be transmitted to neighbouring cells, known as paracrine secondary senescence. Secondary senescence was initially described as a paracrine mechanism, but recent evidence suggests a more complex scenario involving juxtacrine communication between cells. In addition, single-cell studies described differences between primary and secondary senescent end-points, which have thus far not been considered functionally distinct. Here we discuss emerging concepts in senescence transmission and heterogeneity in primary and secondary senescence on a cellular and organ level.

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Evaluation of image reconstruction for mouse brain imaging with synthetic collimation from highly multiplexed SiliSPECT projections

Physics in Medicine and Biology ◽

10.1088/0031-9155/55/17/017 ◽

2010 ◽

Vol 55 (17) ◽

pp. 5151-5168 ◽

Cited By ~ 9

Author(s):

S Shokouhi ◽

D W Wilson ◽

S D Metzler ◽

T E Peterson

Keyword(s):

Image Reconstruction ◽

Brain Imaging ◽

Mouse Brain

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Mito Hacker: a set of tools to enable high-throughput analysis of mitochondrial network morphology

Scientific Reports ◽

10.1038/s41598-020-75899-5 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Ali Rohani ◽

Jennifer A. Kashatus ◽

Dane T. Sessions ◽

Salma Sharmin ◽

David F. Kashatus

Keyword(s):

Single Cell ◽

High Throughput ◽

Data Science ◽

Structural Information ◽

Morphological Changes ◽

Mitochondrial Morphology ◽

Single Cell Level ◽

Mitochondrial Network ◽

Cell Level ◽

Wide Range

Abstract Mitochondria are highly dynamic organelles that can exhibit a wide range of morphologies. Mitochondrial morphology can differ significantly across cell types, reflecting different physiological needs, but can also change rapidly in response to stress or the activation of signaling pathways. Understanding both the cause and consequences of these morphological changes is critical to fully understanding how mitochondrial function contributes to both normal and pathological physiology. However, while robust and quantitative analysis of mitochondrial morphology has become increasingly accessible, there is a need for new tools to generate and analyze large data sets of mitochondrial images in high throughput. The generation of such datasets is critical to fully benefit from rapidly evolving methods in data science, such as neural networks, that have shown tremendous value in extracting novel biological insights and generating new hypotheses. Here we describe a set of three computational tools, Cell Catcher, Mito Catcher and MiA, that we have developed to extract extensive mitochondrial network data on a single-cell level from multi-cell fluorescence images. Cell Catcher automatically separates and isolates individual cells from multi-cell images; Mito Catcher uses the statistical distribution of pixel intensities across the mitochondrial network to detect and remove background noise from the cell and segment the mitochondrial network; MiA uses the binarized mitochondrial network to perform more than 100 mitochondria-level and cell-level morphometric measurements. To validate the utility of this set of tools, we generated a database of morphological features for 630 individual cells that encode 0, 1 or 2 alleles of the mitochondrial fission GTPase Drp1 and demonstrate that these mitochondrial data could be used to predict Drp1 genotype with 87% accuracy. Together, this suite of tools enables the high-throughput and automated collection of detailed and quantitative mitochondrial structural information at a single-cell level. Furthermore, the data generated with these tools, when combined with advanced data science approaches, can be used to generate novel biological insights.

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Cell elastimetry in the detection of antineutrophil antibodies

Blood ◽

10.1182/blood.v57.1.22.bloodjournal57122 ◽

1981 ◽

Vol 57 (1) ◽

pp. 22-24

Author(s):

ME Miller ◽

LA Boxer ◽

EJ Kawaoka ◽

WA Border

Keyword(s):

Single Cell ◽

Immune Complexes ◽

Negative Pressure ◽

Direct Visualization ◽

Cell Assay ◽

Membrane Rigidity ◽

Blind Fashion

Cell elastimetry has been applied to the measurement of antineutrophil antibodies. This technique measures, under direct visualization, the negative pressure required of aspirate PMNs into small-pored pipettes. Two groups of studies were carried out: (A) In the first group of studies, normal PMNs were incubated with 1 of 8 known antineutrophil serums. Each serum significantly decreased membrane deformability-- i.e., cells became more rigid. The study was conducted in an entirely blind fashion. Randomly coded serums from patients and controls were studied for deformability by observers unaware of the code. (B) In the second group of studies, sera containing immune complexes were incubated with normal PMNs. No significant effects were noted upon deformability. As a single cell assay that partially reflects membrane rigidity, elastimetry may, therefore, have potential in the further characterization of mechanisms by which such antineutrophil antibodies compromise neutrophil functions.

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Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects

Nature ◽

10.1038/s41586-019-1414-x ◽

2019 ◽

Vol 572 (7767) ◽

pp. 120-124 ◽

Cited By ~ 43

Author(s):

T. Yvanka de Soysa ◽

Sanjeev S. Ranade ◽

Satoshi Okawa ◽

Srikanth Ravichandran ◽

Yu Huang ◽

...

Keyword(s):

Single Cell ◽

Single Cell Analysis ◽

Cell Analysis ◽

Developmental Defects ◽

Organ Level

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Field of View and Image Distortion : A Review of Low Magnification Imaging In the Environmental and Conventional Scanning Electron Microscopes (SEM)

Microscopy and Microanalysis ◽

10.1017/s143192760001285x ◽

1997 ◽

Vol 3 (S2) ◽

pp. 1193-1194

Author(s):

Brendan J. Griffin

Keyword(s):

Electron Microscopy ◽

Scanning Electron Microscopy ◽

Field Of View ◽

Depth Of Field ◽

Aperture Size ◽

Sem Image ◽

Electron Microscopes ◽

Working Distance ◽

Scanning Electron Microscopes ◽

Scanning Electron

Most scanning electron microscopy is performed at low magnification; applications utilising the large depth of field nature of the SEM image rather than the high resolution aspect. Some environmental SEMs have a particular limitation in that the field of view is restricted by a pressure limiting aperture (PLA) at the beam entry point of the specimen chamber. With the original ElectroScan design, the E-3 model ESEM utilised a 500 urn aperture which gave a very limited field of view (∼550um diameter at a 10mm working distance [WD]). An increase of aperture size to ∼lmm provided an improved but still unsatisfactory field of view. The simplest option to increase the field of view in an ESEM was noted to be a movement of the pressure and field, limiting aperture back towards the scan coils1. This approach increased the field of view to ∼2mm, at a 10mm WD. A commercial low magnification device extended this concept and indicated the attainment of conventional fields of view.

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