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Related Concept Videos

Molecular Shapes01:18

Molecular Shapes

Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.Two regions of electron density in a diatomic...
Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...
Deformations in a Transverse Cross Section01:21

Deformations in a Transverse Cross Section

When a material is subjected to uniaxial stress, it elongates or contracts in the direction of the applied force, and also undergoes changes in the perpendicular directions. This behavior is crucial for understanding how materials behave under stress and is governed by mechanical properties such as Poisson's ratio v, which measures the ratio of transverse strain to axial strain.
As the material stretches, it expands or contracts in orthogonal directions to the load. This phenomenon varies...
Two-Dimensional Microscopy in Microbiology01:29

Two-Dimensional Microscopy in Microbiology

Two-dimensional (2D) microscopy encompasses a range of optical techniques that capture images within a single focal plane, offering detailed representations of microscopic structures. These techniques are essential in biological and medical research, enabling the visualization of cellular and subcellular structures with different levels of contrast and specificity.There are several major types of 2D microscopy, each with strengths and applications.Bright-Field MicroscopyBright-field microscopy...
Three-Dimensional Microscopy in Microbiology01:28

Three-Dimensional Microscopy in Microbiology

Three-dimensional imaging techniques are essential in cell biology, allowing researchers to visualize intricate cellular structures with high resolution. Two prominent methods, Differential Interference Contrast Microscopy (DIC) and Confocal Scanning Laser Microscopy (CSLM), provide distinct advantages for imaging live and thick specimens, respectively.Differential Interference Contrast MicroscopyDIC microscopy enhances contrast in transparent, unstained samples by converting phase...
Space Curves01:25

Space Curves

A space curve describes the path followed by a particle moving through three-dimensional space. Unlike plane curves, which are confined to two coordinates, space curves require three coordinate functions. If t is a parameter, the position of the particle is represented by the vector function\begin{equation*}\mathbf{r}(t)=\langle x(t),y(t),z(t)\rangle,\end{equation*}where x(t), y(t), and z(t) are differentiable functions of t. As t varies over an interval, the endpoints of the position vectors...

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Related Experiment Video

Updated: Jun 22, 2026

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

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Spatial transcriptomics and the anatomical pathologist: Molecular meets morphology.

Jia-Min B Pang1, David J Byrne1, Alice R T Bergin1,2

  • 1Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.

Histopathology
|November 22, 2023
PubMed
Summary
This summary is machine-generated.

Spatial transcriptomics offers detailed molecular insights from tissue sections, revolutionizing anatomical pathology diagnostics. Technologies compatible with formalin-fixed paraffin-embedded (FFPE) tissue are paving the way for routine clinical use.

Keywords:
anatomical pathologyspatial transcriptomicssurgical pathology

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Area of Science:

  • Molecular pathology
  • Genomics
  • Anatomical pathology

Background:

  • Molecular findings are increasingly crucial for anatomical pathology diagnoses.
  • Spatial transcriptomics provides gene expression data with spatial context from single tissue sections.

Purpose of the Study:

  • To review spatial transcriptomics methods, focusing on FFPE compatibility.
  • To discuss data analysis approaches and potential applications in pathology.

Main Methods:

  • Overview of various spatial transcriptomics technologies.
  • Emphasis on platforms compatible with formalin-fixed paraffin-embedded (FFPE) tissues.
  • Discussion of data assessment strategies.

Main Results:

  • Spatial transcriptomics enables high-resolution expression profiling correlated with tissue morphology.
  • Several methods are now compatible with FFPE tissues, broadening accessibility.
  • Potential for integration into routine anatomical pathology workflows.

Conclusions:

  • Spatial transcriptomics is a transformative technology for anatomical pathology.
  • FFPE compatibility is key for diagnostic applications.
  • Further development may lead to routine use in pathology practice.