Introduction to Whole Mouse

Background Recent advances in tissue clearing techniques, combined with high-speed image acquisition through light sheet microscopy, enable rapid three-dimensional (3D) imaging of biological specimens, such as whole mouse brains, in a matter of hours.

Here, we employ spherical matrix array geometry to combine optoacoustic tomography (OAT) and ultrasound localisation microscopy (ULM), and obtain dual-mode volumetric images of the whole mouse brain.

We highlight a petabyte application dataset involving 62 whole mouse brains, from which we identified 50,233 somata of individual neurons, profiled the dendrites of 11,322 neurons, reconstructed the full 3-D morphology of 1,050 neurons including their dendrites and full axons, and detected 1.

In the era of diffraction-limited storage rings, can X-ray nanoimaging be extended to millimetre- or even centimetre-sized specimens such as whole mouse brains? The authors believe so and provide size-dependent imaging time and resource estimates based on calculated flux requirements and recent method developments in related disciplines.

Background Recent advances in tissue clearing techniques, combined with high-speed image acquisition through light sheet microscopy, enable rapid three-dimensional (3D) imaging of biological specimens, such as whole mouse brains, in a matter of hours.

This setup allows ultra-high-resolution images (120 Mpixels in size) of whole mouse organ sections to be obtained, with subcellular resolution and single-particle sensitivity.

In this work, we used whole mouse prostates (organ level) with prostate cancer tumors (sub-organ objects of interest) as example cases, and included quantitative histological features relevant for tumor biology in the VR model.

Therefore, we aimed at establishing a model which allows the study of calcification in intact mouse aortic valves by using the Miniature Tissue Culture System (MTCS), an ex vivo flow model for whole mouse hearts.

Three hours after noise exposure, expression levels of the whole mouse genome in cochleae were analyzed by RNA-seq and DNA microarray.

The exposure of both whole mouse bodies and organs on the super resolution screen surface allowed the radioactivity of the PSMA inhibitor distributed in the tissues to be detected and quantified.

We introduced a cross-modality registration method, called mBrainAligner, which uses coherent landmark mapping as well as deep neural networks to align whole mouse brain images to the standard Allen Common Coordinate Framework atlas.

We highlight a petabyte application dataset involving 62 whole mouse brains, from which we identified 50,233 somata of individual neurons, profiled the dendrites of 11,322 neurons, reconstructed the full 3-D morphology of more than one thousand neurons including their dendrites and full axons, and detected million scale putative synaptic sites derived from axonal boutons.

Here, we isolated AMPAR trafficking vesicles (ATVs) from whole mouse brains via immunoprecipitation and characterized them using immunoelectron microscopy, immunoblotting, and liquid chromatography tandem mass spectrometry (LC-MS/MS).

Cryo-imaging sections and images a whole mouse and provides ~ 120-GBytes of microscopic 3D color anatomy and fluorescence images, making fully manual analysis of metastases an onerous task.

Histological tissue sections of a whole mouse kidney were prepared.

By utilizing these specifications, the microvascular structures in a whole mouse ear could be imaged within 30 seconds without any additional image registration.

Results We screened the EYFP-expressing CRH-IRES-Cre;Ai32 mouse line to reveal the morphologies of individual CRH neurons throughout the whole mouse brain by using a fluorescence micro-optical sectioning tomography (fMOST) system.

We used diffusion tensor magnetic resonance imaging (DT-MRI) with high-speed compressed sensing to generate a tractogram of the whole mouse PNS.

We present a methodological framework suitable for reconstruction of the whole mouse brain cerebral microvasculature by X-ray tomography with the unprecedented pixel size of 0.

3 mm) to cover a whole mouse DRG, with a high pixel resolution of 0.

Here, we show the first super-resolution imaging of flat-mounted whole mouse cornea using single-molecule localization microscopy (SMLM).

In this presentation, we will describe the method in detail and show results from thick samples including intact whole mouse brains and organoids.

Here the authors use a Bessel light-sheet approach combined with a content-aware compressed sensing computational pipeline to image whole mouse organs at subcellular resolution in a few minutes.

We generated imaging data from 15 whole mouse brains to validate atlas performance and observed qualitative and quantitative improvement (37% greater alignment between atlas and anatomical boundaries).

whole mouse tissues) specimens are often not specifically prepared for ultrastructural analyses but simply immersed in liquid nitrogen before long-term cryo-storage.

Consistent modification of primary methods for optical tissue transparency has allowed observation of the whole mouse body at single-cell resolution or thick tissue slices at the nanoscale level, with the final aim to make intact primate and human brains or thick human brain tissues optically transparent.

In the experiments, we evaluate the performance of our method on the challenging 3D neuron images from two datasets, the BigNeuron dataset and the Whole Mouse Brain Sub-image (WMBS) dataset.

Together, these tools provide high-throughput analyses of whole mouse SC and enable direct comparison of 3D spatial information between animals and studies.

This study expands our knowledge of the brain-wide inputs regulating visual areas and demonstrates that our improved rabies virus tracing strategy can be used to scale up the effort in dissecting connectivity of genetically defined cell populations in the whole mouse brain.

The invention of tissue clearing, advances in immunohistochemistry and development of selective plane illumination microscopy (SPIM) now make it possible to acquire whole mouse brain images at submicron spatial resolution with a vast array of cell specific markers [10] [11] [12] [13].

Here, we isolated AMPA-containing vesicles (ACVs) from whole mouse brains via immunoisolation and characterized them using immunoelectron microscopy, immunoblotting, and liquid chromatography–tandem mass spectrometry (LC–MS/MS).

Together, these tools provide high-throughput analyses of whole mouse SC and enable direct comparison of 3D spatial information between animals and studies.

Here, we propose a multimodal neuroimaging pipeline to identify and acquire fiber crossing areas in whole mouse brains.

Mice were inoculated with a lethal dose of recombinant RABV expressing enhanced green fluorescent protein (EGFP) under different infection routes, and a three-dimensional view of the distribution of RABV in the whole mouse brain was obtained using fMOST.

3 mm) to cover a whole mouse DRG, with a high pixel resolution of 0.

Proof-of-principle is demonstrated in whole mouse brain, mouse spinal cord and human white and gray matter samples.

Using TeraVR, we produced precise 3-D full morphology of long-projecting neurons in whole mouse brains and developed a collaborative workflow for highly accurate neuronal reconstruction.

Using quantitative PCR, we found that the whole mouse nodose ganglion was predominantly enriched in the short form of Lepr, rather than its long form.

Using TeraVR, we have produced precise 3-D full morphology of long-projecting neurons in whole mouse brains and developed a collaborative workflow for highly accurate neuronal reconstruction.

High-speed optoacoustic tomography can monitor the neural activity of a whole mouse brain, by using a genetically encoded calcium sensor originally developed for fluorescence microscopy.

Then, color-based automatic segmentation of birefringent components from 3D scanned tissue volume is proposed to isolate the 3D network of the nerve bundles in a whole mouse brain.

We evaluated the suitability for kidney capillary imaging of the nanoparticle-based blood pool contrast agents Aurovist 15 nm and ExiTron nano 12000, along with the vascular casting resin μAngiofil, by post mortem imaging of whole mouse kidneys with 4-5 μm voxel size using the laboratory source μCT system Nanotom m.

While the manual approach is limited to small regions-of-interest in the brain, automated tools are needed to up-scale translational approaches and generate whole mouse brain counts in an atlas framework.

Enzymatic dissociation of four whole mouse aortas was followed by single cell sequencing of over 10,000 cells.

Material and methodsPotential Immunogenic DNA and intracellular components were removed from whole mouse ovaries by agitation in a 0.

Here, I have used single-cell lineage tracing in the whole mouse uterus to demonstrate that epithelial stem cells exist in the mouse uterus.

As an example of how the protocol can be used, we counted the number of cells in an adult whole mouse brain and other distinct anatomical regions and determined the number of cells transduced with mCherry following whole-brain infection with adeno-associated virus (AAV)-PHP.

Here, we report a label-free optical projection tomography (LF-OPT) technique for quantitative whole mouse embryo imaging.

In biodistribution study, NVs spread to the whole mouse body and localized in the lung, liver, and kidney at 6 h.

The result suggests that the model can accurately identify target regions and even the whole mouse brain outline as a special case.

We have updated our previous list of whole mouse brain FMRP mRNA targets with more replicates, deeper sequencing and improved analysis The use of tagged FMRP in less abundant cell populations allowed identification of novel mRNA targets missed in a whole brain analysis.

We have combined these two complementary views of connectomics to build a first draft statistical model of the neuron-to-neuron micro-connectome of a whole mouse neocortex.

Our aim was to identify patterns of electrical rhythmicity in smooth muscle of the proximal region of isolated whole mouse colon and characterize their mechanisms of origin.

The presented methodology enables the characterization of crucial tissue structures in three dimensions and is demonstrated on a whole mouse kidney.

We then extended the application of this algorithm to correct motions to obtain vasculature imaging in the whole mouse back.

Coagulation of whole mouse blood was monitored via a high-frequency ultrasound system with a central frequency of 80 MHz.

We used a transgenic mouse model made with a bacterial artificial chromosome containing the whole mouse Sgk1 gene modified to introduce an activating point mutation.

We built a whole mouse brain model with connectivity derived from tracer studies.

The here introduced clearing protocol termed stabilised DISCO allows to image spines in a whole mouse brain and to detect faint changes in the activity-dependent expression pattern of tdTomato.

Here, we propose the use of a multi-angle-resolved subvoxel selective plane illumination microscope (Mars-SPIM) to achieve high-throughput imaging of whole mouse brain at isotropic cellular resolution.

In 2018, he moved to Japan, first at the National Institute for Physiological Sciences in Okazaki, and a few months later to Keio University School of Medicine in Tokyo, where he had just been appointed Assistant Professor at the time he passed away, working on a comprehensive ultrastructural mapping of the circuitry of the whole mouse brain at a single-synapse level of resolution.