Confocal laser scanning microscopy (CLSM) provides highly detailed 3D structure of biological tissues at cellular and sub-cellular level. In this article we present a data flow which enables the import of CLSM data to sophisticated
animation software, thus enabling the creation of anatomically accurate movies for educational and public engagement purposes. This requires consideration of multimedia and cognitive load theories.
the resources in this section provide information that can assist in creating a cellular visualizations, scenes that require the whole view of a cell, or cellular organelles, where actors are between ~ 30nm and 500um, or provide context for molecular visualizations. The information here includes 2-dimensional structure and dynamics of cells, and organelles, and cytoskeletal and extracellular structures.
Keller, Philipp
Dynamics of building plans of animals from single-cell to whole-organism level (fly, zebrafish, mouse). Quantitative high-speed imaging and multiview dynamics of developing embryos. Lab website: movies, links to references.
Stocker, Roman
Microbiology at the interface between fluid mechanics and microbial ecology. Video microscopy and image analysis to capture and quantify microbial behavior. Topics include: bacterial rheotaxis, phytoplakton holographic microscopy, flagella mechanics, bacterial turbulence and collective behavior, bacterial chemotaxis, biofilms. Lab website: movies, links to references.
Moss, Bernard
Dynamic mechanisms used by viruses to infect cells. Topics include: Vaccinia virion movement, dynamic orthopoxvirus inclusion bodies. Lab website: movies, links to references.
Singer, Robert H
Real-time visualization of transcription kinetics, mRNA transport, and degradation in cells (yeast, fly, human). Quantitative fluorescence data, mathematical modeling. Lab website: visuals, links to references.
Gertler, Frank
Signaling and cytoskeleton dynamics during guided cell movement. Topics include: cancer, axon guidance. Lab website: movies, links to references.
Kirchhausen, Tomas
Dynamic processes that mediate movement of membrane proteins throughout cells. Topics include: clathrin, receptor-mediated endocytosis, secretion. Lab website: movies, visuals, links to references.
Cytokinetic Mafia
Cytokinesis. Movies of cytokinesis from various organisms: E.coli, yeast, Dicty, C.elegans, sea urchin, Xenopus, Zebrafish, rat, etc. (a.k.a. havoc from the Ted Salmon lab)
Theriot, Julie
Microbiology and dynamics of bacterial and fungal pathogens. Topics include: Listeria, Shigella, Salmonella, Candida. Lab website: movies, links to references.
The Bacterial Cytoplasm Has Glass-like Properties and Is Fluidized by Metabolic Activity
A primary research article describing the glass-like properties of bacterial cytoplasm than can be used as a reference for modeling the dynamics of molecules in the cytoplasm.
Individual versus collective fibroblast spreading and migration: regulation by matrix composition in 3D culture.
Fibroblast migration in 3D matrix
Cytotoxic T- Cells on Patrol
Nice video footage of cytotoxic t-cell migration than can be used as a reference for cell migration.
The Cell – An Image Library
The Cell – An Image Library is a repository for microscopy images and videos of eukaryotic and bacterial organelles and macromolecular structures. The images can be used as a reference to infer the 3D structure of organelles and macromolecules, and the videos can be used as reference for the dynamic movement of cellular structures.
Nikon Small World Image Gallery
The Nikon Small World Image Gallery contains winning microscopy images from the Nikon Small World Competition, which recognizing excellence in photography with the optical microscope. While it is not a comprehensive source for reference images, the beautiful, high-quality images may be a source of inspiration.
Nikon Fluorescence Microscopy Image Gallery
The Nikon Fluorescence Microscopy Image Gallery contains high quality 2D fluorescence microscopy images of cells and tissues. These images can be used to infer the 3D structure of cellular organelles, macromolecules (including cytoskeletal components) and tissues.
JCB Cell Biology Image Database
JCB Cell Biology Image Database is a repository for images associated with articles published in the Journal of Cell Biology. The database contains a wide variety of high quality images on many topics in cell biology and may be a useful source of reference imagery.
Neurocytology TEM Atlas
The Neurocytology TEM Atlas contains a collection of Electron Microscopy images specifically focusing on the subcellular and tissue level anatomy of neurons and surrounding brain tissue. These images can be used to infer the 3D structure of cellular organelles and tissues in the brain.
Nanoworld Image Gallery
The Nanoworld Image Gallery contains Electron Microscopy images of subcellular organelles, tissues, cells, and small organisms. These images can be used to infer the 3D structure of cellular macromolecules and organelles, or as a reference for the 3D external structure of small organisms, such as fruit flies.
CDC Public Health Image Library
The CDC Public Health Image Library contains a collection of light microscopy, transmission and scanning electron microscopy images pertaining to public health. Reference images of the external structure of bacteria, viruses, and small organisms can be found here.
Electron Microscopic Atlas of Cells, Tissues, and Organs
The Electron Microscopic Atlas of Cells, Tissues, and Organs is a collection of Electron Microscopic Images of tissues, cells and subcellular organelles. These images can be used to deduce the 3D structure of the respective organelles and tissues.
Human Protein Atlas
The Human Protein Atlas is a histology and immunofluorescence tissue based human proteomics database, containing both normal and cancerous human tissue samples. It can be used to determine where a protein of interest can be found in human tissue.