digital imaging in microscopymicroscopy.berkeley.edu/resources/talks/digital imaging.sm.pdf ·...
TRANSCRIPT
Digital Imaging in Microscopy
Hand DrawingThe Camera Lucida
Film at focal plane of projection lens
Photo tube
Projection Lens
• 4x5" film• 35 mm film
• Black & White filmTechPan 100
• Color filmK25, K64
Film Photography
First PassSecond Pass
∆T = 1/60 s (fields)
Full frame image = 1/30s
Video Imaging — Analog TechnologyDynamic visualization
SignalCurrent
Video SignalVoltage
Target VoltageSupply
10-100v
Target Electrode Photoconductive Layer
Electron beam
Cathode
Filament 525 l
ines
Interlacing
TV Standards
International Television Standards Committee1950s
NTSC, PAL, SECAM
• 525 TV lines• 60 Hz field rate
Realized resolution = 350 horizontal lines
Digital Imaging using Analog Cameras
rateanalog-to-digital
NTSC analog video
Frame grabber
Resultant digital image is 640x480 pixels
Imaging Requirementsfor
Fluorescence Microscopy
Specimen
Excitation filter
Dichroic mirror
A B
Objective
Barrier filter
Fluorescentlight fromsample
Arc light source
Epifluorescence microscope with color image capture
Low-light Image Capture
Increasing Light Sensitivity of Video Detectors
Silicon Intensified Target (SIT) Camera
Vidicon image intensifier
NTSC video<350 lines resolution
Charge Coupled Device (CCD) Detectors
Front-illuminated CCD
Solid State image detectors
Color Imaging — 1 CCD
Analog (0.6 MPix) 1995
1/3” Sony frame transfer CCD
Bayer color filter
Color Imaging — 3 CCDs
1
2
3
CCDsFiltersDichroics
Analog (640x480) Technology1.2MPix
CCD size
Bit Depth and Dynamic Range
8-bit
12-bit
Greater Bit-Depth and Dynamic Range Records More Information
Quantum Efficiency and Spectral Response
QE vs. Impinging wavelength
QE = photons/electrons
Backside-illuminated CCD
Increasing Quantum Efficiency (QE) of CCD
Etching uniformly thins a CCD to a thickness of approximately 10 µm. The image is focused on the backside of the CCD register where there is no gate structure. Thinned CCDs exhibit high sensitivity to light from the soft x-ray to the near-infrared regions of the spectrum.
Coating the CCD can improve the spectral sensitivity of the CCD (top: coated)
Increasing Spectral Response of CCD
Increasing Signal Readout Rate Interline Transfer CCD
Serial Clocks
ParallelClocks
Output Amp
direction of parallel shift
Dark Current and CCD Temperature
Single-Stage Peltier Cooling-10°C ambient
Optronics DEI 450
Photometrics CH350 digital camera
Two-Stage Cooling
Heat from Peltier drawn off by recirculating liquid
Two-Stage Peltier Cooling-35°C to -50°C
Resolution and Sampling
amplitude quantization
N<N>N
Sampling rate (1/T)
Nyquist sampling
1/T > 2f
The rate of sampling must be at least twice the frequency of the resolvable desired structure (signal)
300 dpi 72 dpi 20 dpi
Matching microscope resolution and CCD pixel size
1. Determine microscope resolution d=0.61λ/NA
where NA is the average of the objective and condenser
2. Match the microscope resolution with (a minimum) of two pixels on the CCDM• 0.61λ/NA = 2.0p
where M=the objective magnification; p=pixel sizeor
M = 2p/(0.61λ/NA)
e.g., CCD with 6.8µm pixels and green light (500nm) illumination:M = 2•6.8μ/(0.61•0.5μ/1.3)
M=58Thus, a 60x, 1.3 N.A. microscope objective provides a diffraction-limited image
for the many CCDs (e.g., KAF1401E CCD, QImaging).
Photometrics QuantixKAF 1401E
1035x1317 pixels6.8µm x 6.8µm pixels 12 bit pixel depth5MHz readoutTwo-Stage cooling to -50C
Frame readout CCD
Photometrics CoolSnap HQfor Fast Imaging
1040x1392 pixels12-bit pixel depth6.45µm x 6.45µm pixels 20MHz readoutSingle-stage cooling to -30C
Interline transfer CCD
Sony ICX282 Progressive Scan Interline CCD, Color2560 x 19203.4µm x 3.4µm10-bit20, 10, 5, 2.5MHzPeltier thermoelectric cooling to -10°C below ambient
QImaging MicroPublisher
5 MPixBayer filter CCD
Digital Images
(0,0)
(1024,1024) Blue
Red
Green
E. herbico -la
299R (P fruB -gfp
[AAV])
-3
-2
-1
0
1
2
3
0 2 4 6 8 10 12
cube root [mean pixel intensity]
t=0 (inoculum)
t=4 (leaf #2)
t=25 (leaf #1)t=50 (leaf #1)t=75 (leaf #1)
50
25
105
10.5
75
9095
9999.5
Digital Image Processing and Analysis
Digital Segmentation
and Image Analysis
Some Applications Require 12-16 Bit Dynamic Range
Sarah Swanson, Jones lab PMB
ABA
GA
DIC 440nm fluor ratio
Confocal MicroscopesPoint-Source Detectors (PMT)
Ch 1 (32 PMTs)
Ch 2
Ch 3
pinholesDichroics
Sample Plane
Laser
TransmittedLight detector
diffraction grating
C o n f o c a l M i c r o s c o p y G e n e r a t e s Vo l u m e t r i c D a t a
Software Generates 3D Projections through Volumetric Data
Green: DAPI-stained ChromosomesRed: 5S rDNA
5S sequence marks the end of chromosome 5
3D Projection Using Voxel Data
Ring canals between nurse cells and oocytes
Red:Rhodamine phalloidinBlue: DAPIGreen: FITC-Ab
V o l u m e t r i c D a t a C o l l e c t i o n A l l o w s f o r 3 D I n v e s t i g a t i o n
leech segmented central nervous
system
The nuclei of all the progeny,
neurons and glial cells, are labeled
GFP Expression in Arabidopsis roots
Arabidopsis mutant from J. Haseloff Lab
Feldman lab, PMB
Deconvolution Microscopy
PSF
3D Image Processing and Analysis
Yeast Golgi
Pixel Colocalization
2D histogram
Binary channel
T h e G o l g i A p p a r a t u s
Localization of Golgi and trafficking molecules
Sebastien Carreno, Drubin Lab
Giardia as Imaged using Deconvolution Microscopy
Isosurface modeling
Deconvolved voxel projection
Red: nucleiGreen: fluorescein anti-tubulin