Main Title Slide
Sensing Systems and Signal Processing
Dr Richard
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Bio-imaging applications
microscopy
Optical Microscopy
Micrographia, published in 1665 by
(1635-1703)
Hooke also coined the term cell (compartments in cork)
Microscopy: Scale
Energy (E)
Scattering
Light source
Collimator
Objective lens
Aperture iris
Field iris
Microscope – general schema
Simple optics:
Infinite conjugate imaging
The ratio between the two focal lengths provides magnification
Each lens also performs a 2D Fourier transform – a topic for next year!
Fourier plane
Resolution and numerical aperture
b 1840, d 1905, Jena Germany
acceptance angle
detector array
Simple model of a digital camera:
In some ways, similar to human eye.
Outline the purpose of the visit day
Pixels made of silicon: the charge-coupled device (CCD)
Each “pixel” (picture element) is an independent electronic “box” into which photoelectrons are accumulated before being read out.
The readout process is serial, with charge transferred from pixel to pixel along columns into a read-out register, from where each pixel is quantified to construct an image in X,Y
https://www.leica-microsystems.com/science-lab/introduction-to-digital-camera-technology/
Outline the purpose of the visit day
CCD read out
https://commons.wikimedia.org/wiki/File:CCD_charge_transfer_animation.gif
Several sources of noise contribute to camera images:
Thermal (reduce integration time, cool sensor)
Read noise (imprecision in quantification – increase numbers to quantify)
Shot noise – proportional to square root of population quantified
https://www.leica-microsystems.com/science-lab/introduction-to-digital-camera-technology/
Accessing low signals:
for e.g. electron-multiplying CCD (emCCD)
Outline the purpose of the visit day
https://www.leica-microsystems.com/science-lab/introduction-to-digital-camera-technology/
N channels = N x data
(@ whatever bit depth + rate)
Signal digitisation in camera sensors
Outline the purpose of the visit day
Imaging cells
Bright field microscopy image of a cross section of plant vascular tissue
By John – http://www.3dham.com/microgallery/index.html, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=7297754
Imaging cells
Bright field microscopy image of MDCK cells.
For many cell types the contrast is often poor with bright field. As the cells have similar optical properties to the surrounding medium.
There is a wide range of advanced microscope techniques that can be used to obtain better contrast.
Such as phase contrast, darkfield, polarisation…
https://www.leica-microsystems.com/science-lab/how-to-do-a-proper-cell-culture-quick-check/
Imaging cells
Image of fluorophore stained BPAE cells
Nucleus (DAPI) blue
Actin ( ) (Mitotracker) red
By exciting fluorophores in turn and recording an image composite showing cell components can be constructed.
This method of using fluorophores can be extended to provide super resolution which won the Nobel prize for chemistry in 2014.
http://www.microscopy-uk.org.uk/mag/indexmag.html?http://www.microscopy-uk.org.uk/mag/artoct09/dw-bpae.html
By Andy Nestl – Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=12693849
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