light sheet microscope  (Carl Zeiss)

Journal: PLoS ONE

Article Title: Elastic Free Energy Drives the Shape of Prevascular Solid Tumors

doi: 10.1371/journal.pone.0103245

Figure Lengend Snippet: 3D rendering of an oblate ellipsoidal tumor. The 3D rendering, created using images taken with a light sheet fluorescence microscope, is rotated about the vertical axis in this sequence of images. Blue: Hoechst-stained nuclei; Red: E-cadherin. Scale bar is 90 µm.

Article Snippet: Light sheet fluorescence microscope imaging (for ) was performed on a Zeiss Lightsheet Z.1 microscope with the help of Dr. C. Schwindling at the Zeiss Microscopy Labs in Munich, Germany and (for ) on a custom-built light sheet fluorescence microscope in the lab of Prof. H. Schneckenburger with the assistance of S. Schickinger at the University of Aalen, Germany .

Techniques: Fluorescence, Microscopy, Sequencing, Staining

Journal: PLoS ONE

Article Title: Elastic Free Energy Drives the Shape of Prevascular Solid Tumors

doi: 10.1371/journal.pone.0103245

Figure Lengend Snippet: The various projections of oblate ellipsoidal tumors. a. Projections (maximum intensity) of two oblate ellipsoidal grown in 0.5% agarose gel and imaged with a light sheet fluorescence microscope from four different directions. b . Rotational sequences of the 3D renderings. The 0° orientation is marked with an asterisk in a . Complete sequences are available as Movies S3 S4 . Fluorescence signal is from Hoechst-stained nuclei. Scale bars are all 50 µm.

Article Snippet: Light sheet fluorescence microscope imaging (for ) was performed on a Zeiss Lightsheet Z.1 microscope with the help of Dr. C. Schwindling at the Zeiss Microscopy Labs in Munich, Germany and (for ) on a custom-built light sheet fluorescence microscope in the lab of Prof. H. Schneckenburger with the assistance of S. Schickinger at the University of Aalen, Germany .

Techniques: Agarose Gel Electrophoresis, Fluorescence, Microscopy, Staining

Journal: bioRxiv

Article Title: A versatile tiling light sheet microscope for cleared tissues imaging

doi: 10.1101/829267

Figure Lengend Snippet: The 3D tissue imaging ability evaluation and comparison with a conventional light sheet microscope. (a-c) Lateral and axial maximum intensity projections (MIP) of a cleared Thy1-YFP mouse brain imaged with the presented microscope. (d-f) Lateral and (g-i) axial MIPs of a selected volume (white) in (a) and (b), imaged with a Zeiss Z1 light sheet microscope, a six-tile mode and a non-tile mode of the presented tiling light sheet microscope. (j-l) Zoom in views of the selected areas in (g-i). (m-o) Axial slices through the indicated planes in (j-l). (p,q) 3D renderings of two ~2×2×5 mm 3 subvolumes (yellow and magenta) in (a) imaged with a six-tile mode of the microscope. (r-u) Lateral and axial MIPs of the selected volumes in (p) and (q). (v,w) Axial slices through the indicated planes in (r) and (t). (x,y) Zoom in views of the selected areas in (s) and (u). The size of all inserts in (m-o) is 50×50 μm 2 . Scale bars, 1 mm (b-d), 200 μm (d,g), 50 μm (j,m), 100 μm (r-w), and 10 μm (x,y).

Article Snippet: A conventional light sheet microscope (Zeiss Z1) equipped with a 0.16 NA air objective was first used to image the sample at ~2×2×15 μm3 spatial resolution in ~1.5 hours.

Techniques: Imaging, Microscopy

Journal: bioRxiv

Article Title: A versatile tiling light sheet microscope for cleared tissues imaging

doi: 10.1101/829267

Figure Lengend Snippet: The tiling light sheet microscope for cleared tissue imaging. (a,b) Either the spatial resolution or the imaging speed is decreased when a large sample is imaged with conventional LSM. (c) Both the high spatial resolution and the high imaging speed are maintained by using tiling light sheets. (d) Both the size of the FOV and the excitation tiling light sheet can be adjusted based on the desired the spatial resolution and imaging speed. (e,f) The schematic diagram and configuration of the tiling light sheet microscope. (g) The generation of binary phase maps used to modulate the illumination light. Tilt 1 phase is used to control the excitation laser beam intensity profile. Tile 2 phase is adjusted to keep the excitation light sheet in focus within the FOV. Defocus phase is used to tile the excitation light sheet and to correct the light sheet lateral drifting caused by RI variation of the imaging buffer. All phase components are superimposed and binarized before being shifted to correct the tilt of the excitation beam.

Article Snippet: A conventional light sheet microscope (Zeiss Z1) equipped with a 0.16 NA air objective was first used to image the sample at ~2×2×15 μm3 spatial resolution in ~1.5 hours.

Techniques: Microscopy, Imaging

Journal: bioRxiv

Article Title: A versatile tiling light sheet microscope for cleared tissues imaging

doi: 10.1101/829267

Figure Lengend Snippet: The 3D tissue imaging ability evaluation and comparison with a conventional light sheet microscope. (a-c) Lateral and axial maximum intensity projections (MIP) of a cleared Thy1-YFP mouse brain imaged with the presented microscope. (d-f) Lateral and (g-i) axial MIPs of a selected volume (white) in (a) and (b), imaged with a Zeiss Z1 light sheet microscope, a six-tile mode and a non-tile mode of the presented tiling light sheet microscope. (j-l) Zoom in views of the selected areas in (g-i). (m-o) Axial slices through the indicated planes in (j-l). (p,q) 3D renderings of two ~2×2×5 mm 3 subvolumes (yellow and magenta) in (a) imaged with a six-tile mode of the microscope. (r-u) Lateral and axial MIPs of the selected volumes in (p) and (q). (v,w) Axial slices through the indicated planes in (r) and (t). (x,y) Zoom in views of the selected areas in (s) and (u). The size of all inserts in (m-o) is 50×50 μm 2 . Scale bars, 1 mm (b-d), 200 μm (d,g), 50 μm (j,m), 100 μm (r-w), and 10 μm (x,y).

Article Snippet: A conventional light sheet microscope (Zeiss Z1) equipped with a 0.16 NA air objective was first used to image the sample at ~2×2×15 μm3 spatial resolution in ~1.5 hours.

Techniques: Imaging, Microscopy

Journal: bioRxiv

Article Title: A versatile tiling light sheet microscope for cleared tissues imaging

doi: 10.1101/829267

Figure Lengend Snippet: The tiling light sheet microscope for cleared tissue imaging. (a,b) Either the spatial resolution or the imaging speed is decreased when a large sample is imaged with conventional LSM. (c) Both the high spatial resolution and the high imaging speed are maintained by using tiling light sheets. (d) Both the size of the FOV and the excitation tiling light sheet can be adjusted based on the desired the spatial resolution and imaging speed. (e,f) The schematic diagram and configuration of the tiling light sheet microscope. (g) The generation of binary phase maps used to modulate the illumination light. Tilt 1 phase is used to control the excitation laser beam intensity profile. Tile 2 phase is adjusted to keep the excitation light sheet in focus within the FOV. Defocus phase is used to tile the excitation light sheet and to correct the light sheet lateral drifting caused by RI variation of the imaging buffer. All phase components are superimposed and binarized before being shifted to correct the tilt of the excitation beam.

Article Snippet: A conventional light sheet microscope (Zeiss Z1) equipped with a 0.16 NA air objective was first used to image the sample at ~2×2×15 μm3 spatial resolution in ~1.5 hours.

Techniques: Microscopy, Imaging

Journal: Frontiers in Physiology

Article Title: Optimization of Whole Mount RNA Multiplexed in situ Hybridization Chain Reaction With Immunohistochemistry, Clearing and Imaging to Visualize Octopus Embryonic Neurogenesis

doi: 10.3389/fphys.2022.882413

Figure Lengend Snippet: Overview of experimental pipeline for Octopus vulgaris embryos. RNA in situ hybridization chain reaction version 3.0 (RNA-ISH) and immunohistochemistry (IHC) are followed by fructose-glycerol clearing and imaging with Light Sheet Fluorescence Microscopy (LSFM). The final images (3D images and Z-stack planes) as well as videos are acquired, processed and analyzed with ZEN (black edition) and ARIVIS VISION4D v.3.1.4 software. For developmental stage XV embryo (its size is approximately 1,25 mm x 0,88 mm), RNA-ISH Clearing Imaging Image Analysis takes approximately 7 days whereas, RNA-ISH IHC Clearing Imaging Image Analysis takes around 9 days. (This figure is designed using a resource from freepik.com ).

Article Snippet: Imaging was done using Zeiss Z1 Light sheet fluorescence microscopy (LSFM) (Carl Zeiss AG, Germany).

Techniques: RNA In Situ Hybridization, In Situ Hybridization, Immunohistochemistry, Imaging, Fluorescence, Microscopy, Software

Journal: Frontiers in Physiology

Article Title: Optimization of Whole Mount RNA Multiplexed in situ Hybridization Chain Reaction With Immunohistochemistry, Clearing and Imaging to Visualize Octopus Embryonic Neurogenesis

doi: 10.3389/fphys.2022.882413

Figure Lengend Snippet: Whole Mount HCR v3.0 followed by fructose-glycerol clearing on an Octopus vulgaris embryo (developmental stage XV) imaged with LSFM. Top panel illustrates the merged 3D view from the posterior side of the embryo, and bottom panel shows a single plane of a coronal section. (A) Overview image showing the expression of Ov-elav and Ov-apolpp on a Stage XV embryo in 3D. Note that only high-level expression is retained on the merged view. DAPI (in grey) is used for nuclear labelling. (B–D) 3 individual channels from (A) . (E) Overview image showing the expression of Ov-elav and Ov-apolpp on a coronal section of Stage XV embryo. (F–H) 3 individual channels from (E) . Abbreviations: ar, arm; D, dorsal; ey, eye; fu, funnel; gg, gastric ganglion; LL, lateral lip; ma, mantle; n, neuropil; OL, optic lobe; SEM, supraesophageal mass; sg, stellate ganglion;SUB, subesophageal mass; V, ventral; y, yolk.

Article Snippet: Imaging was done using Zeiss Z1 Light sheet fluorescence microscopy (LSFM) (Carl Zeiss AG, Germany).

Techniques: Expressing

Journal: Frontiers in Physiology

Article Title: Optimization of Whole Mount RNA Multiplexed in situ Hybridization Chain Reaction With Immunohistochemistry, Clearing and Imaging to Visualize Octopus Embryonic Neurogenesis

doi: 10.3389/fphys.2022.882413

Figure Lengend Snippet: Whole Mount multiplexed HCR v3.0-IHC followed by fructose-glycerol clearing on an Octopus vulgaris embryo (developmental stage XV) imaged with LSFM to visualize neurogenesis. (A) Overview image showing the expression of Ov-ascl1 and Ov-neuroD and presence of mitotic cells (PH3+) on a Stage XV embryo in 3D view. DAPI (in grey) is used for nuclear labelling. (B) Image illustrating mitotic PH3+ cells with DAPI which is an indication of successful IHC after HCR. (C) Multiplexed HCR Image of Ov-ascl1 and Ov-neuroD with DAPI. (D–G) Separate channels from (A) . (H) Overlay of Ov-ascl1 and Ov-neuroD show mutually exclusive expression. Yellow line indicates the transition zone area. (I) Overview image showing the expression of Ov-ascl1 and Ov-neuroD and presence of mitotic cells (PH3+) on a coronal section of Stage XV embryo. (J–M) 4 individual channels from (I) . Abbreviations: ar, arm; D, dorsal; ey, eye; fu, funnel; LL, lateral lip; ma, mantle; OL, optic lobe; SUB, subesophageal mass; V: ventral; y, yolk.

Article Snippet: Imaging was done using Zeiss Z1 Light sheet fluorescence microscopy (LSFM) (Carl Zeiss AG, Germany).

Techniques: Immunohistochemistry, Expressing