Biological Imaging I - Lecture Slide - Biology 1, Slides of Biology

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Computational Biology, Part 21

Biological Imaging I

G. Steven Vanni

Robert F. Murphy

Biological imaging

 Significant advances in the fields of optics and

electronics in the past two decades have greatly

increased the utility of imaging for addressing

biological questions.

 These advances permit

 more diverse types of information to be extracted from

biological specimens

 with greater accuracy

 and under more demanding conditions.

 On the following two slides are images

demonstrating the capabilities of biological

imaging.

Image acquistion and analysis can produce data to test a hypothesis  This experiment supports the hypothesis that the motor protein, myosin II, (high concentration shown in red) plays a role in separating daughter cells following cell division.

Imaging by Robin DeBiaso

Biological specimens present unique challenges and advantages  Challenges Controlled environmental conditions are required to preserve processes and signals within a biological specimen. It can be difficult to gain physical access to the desired region of a specimen.  Advantages Biological specimens present unique opportunities for the use of chemical and molecular biological probes to detect signals.

Physical and optical accessibility  High magnification (40 to 200X) is often desirable, and this sets limits on how deeply into the specimen images may be acquired.  Typical limits range from 1 mm to 0.1 mm.  Given such limits, specimens must be prepared in ways which allow the optics of the microscope to closely approach the area of interest within the specimen.  Additionally, some specimens absorb or scatter the signal being detected.

 Imaging relies on generating a detectable signal which can be used as a measure of a property of interest in the specimen.  This property of interest is the initial signal, but it must be transduced or changed through several forms before it becomes detectable. Chemical and molecular biological probes may be targeted within a specimen

Image Formation and Acquisition  Having an understanding of the specimen, the next step is the formation and acquisition of a digital image  A two dimensional image plane consists of a rectangular grid of points, or pixels

Grid

Specimen

Pixel

 A digital image plane is acquired by recording a digital value proportional to the intensity of light (or other form of energy) impinging on each pixel of a detector  This intensity usually corresponds to the amount of light emitted by or reflected from a corresponding point on a specimen 0 0 0 2 1 0 0

Projection of specimen

onto dectector grid

Image

Specimen

Image Formation and Acquisition

Display of pixel values  A pixel value is just a number in the data set representing a digital image.  Pixel values may be displayed in different ways, determined by a look up table (LUT). 0 0 0 2 1 0 0

Pixel values Hot to cold

Arbitrary

Binary

LUT

LUT

LUT

Image Formation

 Biological images may be acquired via a

variety of imaging modes or modalities

 Each mode is a combination of an image

formation system and a detector