Biophotonics and Bioimaging Overview

Optical imaging technique where light passes through a sample and is detected on the other side.

A type of photon in transmission imaging that travels in a straight line through the sample without scattering.

A type of photon in transmission imaging that undergoes some scattering but mostly travels in the forward direction.

A type of photon in transmission imaging that undergoes a lot of scattering and takes a highly indirect path through the sample.

A method to improve the quality of transmission images by selectively allowing only photons that travel in a straight line (ballistic photons) to reach the detector.

A method to selectively filter out scattered light in transmission imaging by using polarized light.

Biological tissues are very good at absorbing and scattering light. This makes it challenging to get clear images using transmission methods.

Ballistic photons provide the most detailed information about the sample because they travel through the sample without scattering.

A technique used in optical imaging where the sample is illuminated with a short pulse of light, and an optical gate is used to select only ballistic and snake photons based on their arrival time, allowing for separation of these photons from scattered light.

Optical imaging technique that uses the light reflected back from the sample to create images.

Technique used in reflection imaging to separate coherently backscattered light from multiply scattered light, using a pinhole to filter spatial information.

A technique that uses interference between a reference signal and backscattered light to image a surface, a type of reflection imaging.

A technique that utilizes the emission of light from a substance after it absorbs light of a shorter wavelength.

The molecule responsible for fluorescence.

A process where a fluorophore is attached to a specific molecule in a sample, allowing for the visualization of specific structures.

A technique that uses fluorescent molecules to study the structure and dynamics of biological samples.

The energy of the excitation light used in fluorescence microscopy is always greater than the energy of the emitted fluorescence light.

The ratio of the signal from a fluorescent molecule to the background noise.

A technique used to study the interactions between molecules in a sample.

The ability of a microscope to distinguish between two closely spaced objects.

A fluorescence imaging technique where two low-energy photons simultaneously excite a fluorophore, producing a localized fluorescence signal. This allows for 3D imaging without a pinhole.

The process of generating images by combining multiple layers of data, each representing a thin slice of the sample.

The ability to distinguish between two closely spaced points in an image.

The depth to which light can penetrate into a sample before being absorbed or scattered.

The ability to focus the excitation light to a very specific point in the sample, which reduces background noise and improves image quality.

A method that uses the time delay and intensity of back-scattered light to create images of internal structures. It's similar to ultrasound but uses light instead of sound waves.

A microscopy technique that uses the phase shift differences in light passing through a sample to create contrast. It allows visualization of transparent specimens by converting phase variations to amplitude variations.

A type of microscopy where only light diffracted or refracted by the sample reaches the objective lens, creating bright objects on a dark background.

A microscopy technique where the sample is illuminated with a specific wavelength of light that causes certain molecules to fluoresce, emitting light at a longer wavelength.

The degree to which a substance bends light. Different materials refract light at different angles, making them appear distinct under a microscope.

Light that passes straight through a sample without being scattered or diffracted. It contributes to the background signal in microscopy.

Light that is bent or scattered as it passes through a sample. It contains information about the sample's structure and can be used to create contrast in images.

A specialized plate in a phase contrast microscope that alters the phase and amplitude of the direct light, bringing it in phase (or out of phase) with the diffracted light.

A device that focuses light onto the sample in a microscope. In phase contrast microscopy, the condenser forms a hollow cone of light.

A microscope component that collects light from the sample and forms an image. It plays a crucial role in filtering and focusing the light, making details visible.

The point where two waves overlap and interfere. In phase contrast microscopy, interference between direct and diffracted light creates contrast in the image.

The depth resolution in OCT is determined by the coherence length of the light source. A shorter coherence length results in better depth resolution, allowing you to see finer details within the sample.

The 'zoom' or focus of OCT is limited by the size of the light beam hitting the sample. A smaller beam size leads to better transverse resolution, allowing you to see finer details across the sample.

By combining OCT with a moving platform that scans the sample in three dimensions (X, Y, Z), a 3D image of the sample can be created. This provides a detailed, volumetric view of the sample's internal structure.

Adding a pinhole (a small opening) to the OCT system further enhances the depth resolution by allowing only light from a specific depth to pass through. This helps to reduce noise and improve image clarity.

A specialized light source with a narrow bandwidth and high coherence length needed for OCT. Compared to LEDs, superluminescent diodes provide a more focused and 'coherent' beam of light, crucial for precise measurements in OCT.

A critical component in OCT. The reference mirror reflects a portion of the light beam, allowing interference with scattered light returning from the sample to create a coherent signal.

The ability to see changes in the sample in real-time. OCT can capture images rapidly, allowing us to observe dynamic processes within tissues and cells over time.

OCT provides high resolution compared to traditional ultrasound techniques. This allows for more detailed visualization of fine structures in the biological samples.

Optical Coherence Tomography can be easily integrated into catheters and endoscopes due to its fiber-optic design. This allows OCT imaging to be performed in hard-to-reach areas of the body.

A technique that uses the color (wavelength) of light emitted from a fluorescent marker attached to a sample to differentiate and study different components or processes within the sample.

A technique that uses two fluorescent markers (donor and acceptor) positioned close together within the sample. When the donor fluorophore is excited by light, its energy is transferred to the acceptor fluorophore, leading to a change in fluorescence. This change is used to study interactions between molecules, such as protein-protein interactions.

The proximity between the donor and acceptor fluorophores in FRET is critical. If the distance is within 10 nanometers, energy transfer can occur, allowing the study of very close molecular interactions.

In FRET imaging, the intensity ratio of the donor to acceptor fluorescence (IA/ID) is calculated at each point in the sample. This ratio provides information about the interaction or proximity of the two molecules labeled by the fluorophores.

Spectral and time-resolved imaging techniques are particularly useful for observing and studying biological processes that occur in real-time. These methods can capture changes in fluorescent signals over time, providing insights into dynamic events within cells or tissues.

Spectral and time-resolved imaging techniques are often used in conjunction with epi-fluorescence and confocal microscopy. These techniques offer complementary capabilities and can be combined to provide a more complete understanding of biological samples and processes.