Glossary

Autofluorescence: Is the natural emission of light by biological structures when they absorb light.

Brain vasculature: A summarizing term to include all blood vessels in the brain.

Cell: Cells are the basic building blocks of your body. Each cell has a membrane, which is like a skin that holds everything together, a nuclei, which is the main structure that holds information, and some cytoplasm,  which is liquid. Find out more about cells here.

Channel merging: When we work with multiple tissues of interest (for example blood vessels and brain cells), we are able to individually mark or visualize these for easier identification in an image (for example one can be green, the other red). We are then able to “merge” these separate “channels” containing red and green information and study how these two tissues of interest interact.

Cubism: Art movement of the early 20^th century that resulted in images being fragmented and abstracted. For example, Pablo Picasso was a driving force in this movement.

DNA: DNA (or long form: Deoxyribonucleic acid) holds information about organism development, survival, and health. Simplified, it is the blueprint of your body which is contained in almost every cell of your body.

Dorsal view: Looking at the fish from the back, i.e., looking at posterior/back of the body.

Duct of Cuvier: Is a vein that carries blood cells towards the heart in early developing embryos.

False colour: This is similar to when we edit photos on a smart phone. We are able to change the look on an image by changing certain filters to highlight areas of specific interest. The application of these colours or filters is what we call false colour.

Fluorescence:  Is a process where shorter-wavelength light is taken up by a fluorophore such as a protein (excitation). As the protein is then “charged” with energy, the protein releases some the absorbed energy as longer-wavelength light (emission).

Macrophage: Is a type of white blood cell that removes microorganisms and dead cells. They are part of the immune system and play important roles in tissue health.

Markers: When we look at a tissue under the microscope, it is difficult to see anything. So, to distinguish cells or tissues such as brain cells we need to stain or mark these specifically. There are various ways to do this, but most commonly stains/dyes and genetic methods are used.

Maximum intensity projection: Is form a three-dimensional visualization tool. We are able to take multiple images (12 – 500) of a single item from different focal points using specific microscopes. These individual images can then be compressed together to create one final image. This is called the “maximum intensity projection” which allows us to see an object in much more detail.

Micrometre: A micrometre is a 1/1000 of a millimetre. As an example, 700 micrometre is the thickness of a credit card and about 10 micrometre is the thickness of a single spider silk strand.

Microscope: A microscope is an instrument that allows you to see things that are too small to see with the naked eye. There are various types of microscopes, ranging from simple to incredibly sophisticated and expensive. Read more here. Find out more about: AiryScan –  and Light-Sheet Fluorescence Microscope.

Müller Glia: Specific cell type that is only found in the eye and acts not only to support other cells in the tissue but fulfil other important functions to keep the eye healthy.

Nuclei: Cell compartment that contains the DNA.

Plan-Apochromat: To magnify items of interest with a microscope, a combination of lenses is used and combined, which is called an objective. These objectives can have different properties. Read more about objectives here.

Planes: When we look at our data through a microscope the fish are 3D. To be able to focus throughout the tissue we take many consecutive images while focusing on the fish. The data that we produce are 3D and made of 12-500 single planes.

Retina: The light-sensitive tissue at the back of your eyes.

Scientific complementary metal-oxide semiconductor detection unit: Just like different smart phones have different cameras, different microscopes can have different cameras or detectors. This “Scientific complementary metal-oxide semiconductor detection unit” is a very specific type of detector.

Segmentation: Process of separating objects based on differences and/or similarities. For example, separating up all apples and oranges on a plate. In image analysis, we use segmentation to extract objects of interest. For example, to separate blood vessels from brain tissue.

Signal: Simplified, a signal is information that is higher than background noise. For example, imagine a room full of people chatting (background noise) then a bell ringing (signal). Ideally, the signal is more prominent than the background and easily identified. In microscopy, we often stain tissues to obtain a specific signal.

Support Cells: Cells that fulfil functions in support of other cells, for example cells that provide structural strength.

Transgenic line: A transgenic line is a line of fish that has had their genomes altered for the purpose of studying gene functions. For example, we can use this method to show blood vessels under a microscope using fluorescence.

Ventral view: Looking at the fish from the front, i.e., looking at anterior/front of the body.

Voronoi diagram: Is a method to ascertain how much space is around a given object.

Zebrafish: Fresh water fish that are used in scientific research. Learn more here.