3D Electron Microscopy - UZH - Center for Microscopy and ... · PDF file3D Electron...
Transcript of 3D Electron Microscopy - UZH - Center for Microscopy and ... · PDF file3D Electron...
3D Electron Microscopy:a collection (intro) of methods...
Scientific Center of Optical & Electron Microscopy (ScopeM), [email protected]
1. Little EM History
2. SEM vs. TEM...
3. LM vs EM / confocal?...
4. 3D EM methods for beam transparent (thin specimen) - volume and surfaces
5. 3D EM methods for thick specimen
- small volume vs. large volume
- destructive vs. preservative
6. Discussion
History: Geschichte der Elektronenmikroskopie.... began in Berlin 1931...
Ernst Ruska Max Knoll Bodo von Borries
First transmission electron microscope 1933
Ernst Ruska * 1906 in Heidelberg† 1988 in Berlin
Nobel Price in Physics 1986
History Electron Microscopy.... 1933...das “Übermikroskop”....
1936-40: mµ.....nm!!!
Modern Electron Microscope....
Tools for Studying theNano-Cosmos:
Scanning-force & Scanning-tunnelingMicroscope (SPM)
Field-Ion Microscope/ Atom Probe(1955 E.W. Müller - first image of an atom!)
X-ray diffraction &-microscope
Ion (He-) Microscope
Scanning Electron Microscopy: SEM
• Surface morphology (length, surface, width, depth, height)
• Element/Chemistry (X-ray, Auger, EBSD)
Jeol JSM-7401F
A virtual image built pixel by pixel is formed!
Transmission electron microscope (TEM)Zeiss LIBRA®
120
• Internal morphology (length, surface, width, depth, relation)
• Element/Chemistry (X-ray, EELS, Auger)
A real image is formed by lenses....
Wavelengths of Electrons
Vacc / kV Nonrelativistic wavelength [nm]
Relativistic wavelength [nm]
1 0.0388 0.0388
40 0.00613 0.0060
100 0.00386 0.00370
300 0.00223 0.00197
1000 0.00124 0.00087
Accelerating voltages: SEM 0.5 – 30 kV TEM 100 – 1‘000kV
(Atomic distances: ~ 0.1 nm (Å))
! Imaging Modes - LM vs. EM: (Light vs. Electron Optics)
! Ernst Abbe: Resolution Power
! Angular aperture of the lens - The aperture thus controls the ability of the lens to gather information about the object e.g. the eye at 25 cm corresponding to an angle of about 0.9° for a 4 mm exit pupil diameter of the eye lens; a typical LM with an oil immersion objective lens has 2α of ~175°). For EM typically 8-10mrad (0.5-0.9°)
λ 400nm:
d eye = 0,02-0.1mm
d LM = λ/2 (200nm)
λ 0,004nm (100keV):
d EM = 0,2-0,1 nm!!!λLM/λEM = 100’000x -> Resolution only 1000x better
www.microscopyu.com
! Obtainable resolution: (Electron vs. Light Optics)
λ 400nm:
d eye = 0,02-0.1mm
d LM = λ/2 (200nm)
λ 0,004nm (100keV):
d EM = 0,2nm!!!Sub-Angstrom (corrected EM)λLM/λEM = 100’000x -> Resolution only 1000x better
! Angular aperture for EM typically 8-10mrad (0.5-0.9°)
LM perfect objective lens
! magnetic fields not homogeneous!
3D - Beam Transparent: Confocal Imaging -> optical sectioning in Light Microscopy....for EM?
! EM: - you need a high convergent beam -> Cs Corr.- a “beam transparent” specimen (<50-100nm)- high contrast sample....
! z-slice imaging possible for solid state material Lit: J.J. Einspahr, P.M. Voyles Ultramicoscopy 106, 2006 “Prospects for 3D, nanometer-resolution imaging by confocal STEM” & M. Varela et al. - Annual Review of Material Research 35, 2005 “Material characterization in the aberration-corrected STEM”
! => for all other samples we need other approaches
10 nm
100nm
1 nm
MolecularTEM
Objects “thin”e--transparent
CellularEM
1µ
Objects “thick”not e--transparent
EM in Life-Science: Cellular & Molecular....
“thin” section
3D Electron Microscopy
10nm
100nm
1
“thin”e--transparent => “Tomography”
(various angle views..)
“thin” => tilt series
-> virtual imagestack
1
“Thick”not e--transparent=> serial section
real section or “en-bloc”
section projections or bloc-face view
=> Image Stack
! 3D - Beam Transparent EM
! EM: - macromolecular complexes (helices...)- 2D crystals (protein crystals)- symmetrical objects (icosahedral viral particle)- single particle (isolated > 100k Da)- tomographic reconstruction - tilt series
! collect as many view angle as possible - use Fourier space maths or tomographic procedure to reconstruct 3D volume
! 3D - Beam Transparent EM!
W. Wriggers....
! 3D - Beam Transparent EM! EM: macromolecular complexes (helices...)! -> cylindrical coordinate (real and reciprocal space)! -> different view angle immanent to helical structure
arrangement (periodic in axial rise, pitch and repeat)! -> selection of layer lines and use of Bessel function
Real space / Fourier spaceReal space Fourier (reciprocal) space
FT
FT-1
Images Diffractogram(power spectrum))
1D-lattice
Real space / Fourier spaceReal space Fourier (reciprocal) space
FT
FT-1
Images Diffractogram(power spectrum))
1D-lattice
Helical-”lattice”
Real space / Fourier spaceReal space Fourier (reciprocal) space
FT
FT-1
Images Diffractogram(power spectrum))
1D-lattice
Helical-”lattice”
Knupp&Squire; J. Appl. Cryst. (2004). 37, 832±835
! 3D - Beam Transparent EM! EM: - 2D crystals (protein crystals)! -> e-diffraction (amplitude) or FT of real images (amplitude &
phase)...! -> periodic structure (real and reciprocal space)! -> collect different view angle - tilt series! -> add in fourier space the layers to a 3D frequence
representation!
Real space / Fourier spaceReal space Fourier (reciprocal) space
FT
FT-1
Images Diffractogram(power spectrum))
1D-lattice
2D-lattice
FILTER MASK
Averaging by crystallographic methods (Fourier space)
DIFFRACTOGRAMRAW DATAPICTURE
WITH REGULARSTRUCTURE
ANDNOISE
LASER
LENS
LENS
Diffraction of a coherentparallel light beam bya regular object generatesparallel beams emanatingoff axis
A filter, ajusted to the regularspots, separates their lightfrom the noise.A second lens creates thefiltered image
Focusing of parallel wavesin phase, corresponding toregular structure on the pictureleeds to small regularly arrangedspots in the focus plane, whilenoise is focused elsewhere
LASER
RAW DATAPICTURE
WITH REGULARSTRUCTURE
ANDNOISE
LENS FILTERSCATTERED ANDFOCUSED NOISE
LENS
FILTERED IMAGESHOWINGREGULARSTRUCTURE
WITHOUT NOISE
Diffraction of a coherentparallel light beam bya regular object generatesparallel beams emanatingoff axis
A filter, ajusted to the regularspots, separates their lightfrom the noise.A second lens creates thefiltered image
Focusing of parallel wavesin phase, corresponding toregular structure on the pictureleeds to small regularly arrangedspots in the focus plane, whilenoise is focused elsewhere
AVERAGING OF REPETITIVE MOTIFS BY CRYSTALLOGRAPHIC METHODS
NOISE
“optical” Fourier Filtering ...
1st order
2nd order
e.g. TEM Negative Film
“in-silico” (Com
puter)
contour map of structure
real space
Averaging by crystallographic methods (Fourier space)
Laser, FT
well orderedareas
Analog
inverse Fourier transform
Four
ier t
rans
form
reciprocal space
Fourier Filtering in-silico
Cross correlation averaging (real space)
2D-crystal
Real Space Filtering (in-silico)
Image enhancement: signal, noise and averagingimproving the signal-to-noise ratio
Image:sum of signaland noise
First 3D-reconstruction from a protein-complex(in fourier space)
Baker, Henderson (2001)
Already 1975 Henderson et al used a combination of averaging technique by the use of 2D protein-crystals -> to enhance the signal to noise ration to “see” one single unit in one projection view...
- By tilting such 2D protein-crystals they were able to collect over more than 7-15 years enough data with high resolution of the “identical” protein with good S/N ration from various tilt angles...
- By collecting different tilt angle -70° to +70° they were able to use tomographic reconstructions to reconstruct a 3D view...
Tomography
The word tomography is composed of the greek words tomé (to section) and gráphein (to write, to draw) and means recording an image of a section through an object.
Tomography is a mathematical technique that reconstructs a certain property of the object from a series of integrals of this property. (e.g. Z-scattering or phase shift properties in transmission images of the object)
Schematic diagram to illustrate the principle of 3D-reconstruction (Fourier space)
Baker, Henderson (2001)- by TEM imaging... - in-silico (PC)...
3D-volume reconstruction: 2D-crystalsPurple membrane (biological solar cell)
3D-model of BacteriorhodopsinTilt series reconstructionresolution: x,y: 3.5Å; z: 5ÅUnwin und Henderson 1975-1990 Contour map of the projected structure
Licht
15Å
Halo-bacteriumhalobium
1µ
! 3D - Beam Transparent EM
! EM: single particle (isolated > 100k Da) & tomographic reconstruction - “tilt series”
! -> collect as many images and projection of your sample (real)! -> > 100’000 images of single particle (statistics)! -> Multivariate statistics selects “classes” of different projection
views! -> average n particles per class -> merge 2D transfers in 3D in
Fourier space -> back-transformation (rFFT)
3D-volume reconstruction: single particlesCa-release channel (2'400 kD)
preparation: “frozen-hydrated”TEM: -180°C, high defocus
3D-Reconstruction
-Digitization-ctf-correction (flipping phases)-particle selection and cutting-particle alignment (different reference images)-particle classification MVA (x,y,z, α,β,γ)-averaging (identical projections, class averages)-angle assignment, 3D-reconstruction
Orlova, Wah Chiu (1996)
Electron Tomography - macromolecular complexes..
2D-projections of single particlesa random series of 2D-images
aligned by man/computer selection-> selection of different
projection classes of images-> Tomographic reconstruction
2D-projection tilt seriesby using inherent
tilted specimen entities (helical structures) or by collecting tilt series (2D crystals).
-> TEM “Tomography”
3D-volume reconstruction: single particlesoverview of the various iterative refinements
Electron Tomography - macromolecular complexes..
2D-projections of single particlesa random series of 2D-images
aligned by man/computer selection-> selection of different
projection classes of images-> Tomographic reconstruction
2D-projection tilt seriesby tilting the specimen stage...
-> TEM Tomography
(question of S/N...)
Electron tomography “weighted back projection (real space)-> generate direct tilt series...(S/N!!!)
2D-projectionsa 3D-object is projected at various tiltangles into a series of of 2D-images
-> by TEM Imaging!
3D-reconstructionto reconstruct the 3D-object all thebackprojection bodies are summed
-> by Computer (in-silico)
W. Baumeister, MPI Martinsried -> more by Ohad Medalia
Crowther criterion Elongation factor
Missing wedge
Fourier Space
d = lateral resolutionD = thickness of sampleN = number of projectionsα = missing wedge angle
α
EM Tomo: resolution and weighting
Lit.: see also S.Nickel et al..., Nature Reviews Molecular Cell Biology....
Electron Tomography - macromolecular complexes..
2D-projections of single particlesa random series of of 2D-images
aligned by man/computer selection-> selection of different
projection classes of images-> Tomographic reconstruction
2D-projection tilt seriesby tilting the sepcimen stage...
-> TEM Tomography
Classical Tomography:
only images along one rotation axis....
Single particle imaging Tomography:
images randomly over the entire spheres .....
“The projection angle sphere”....! 3D - Beam Transparent EM
! TEM: - macromolecular complexes (helices...)- 2D crystals (protein crystals)- symmetrical objects (icosahedral viral particle)- single particle (isolated > 100k Da)- tomographic reconstruction - tilt series
! collect as many view angle as possible - use Fourier space maths or tomographic procedure to reconstruct 3D volume
Tomography (cellular TEM)tilt series (same specimen area)averaging not possibleresolution: 100-50Å
Single particlesMW >250kDtilting not necessaryaveraging (after classification)resolution: 20-10Å
1D-crystals (helices)tilting not necessaryaveragingresolution: 30-10Å
2D-crystals tilt series (different crystals)averagingresolution: 20-3Å
Flow diagram 3D (cryo-) TEMfrom sample preparation to 3D-map interpretation
H. Gross...
Alternative ways to extract 3D structure on macro-molecular complexes... ...
T4-Polyhead: freeze-dried and unidirectionally shadowed with TaW (5Å)
Surface relief reconstruction - TEM
reconstructed surface reliefTEM-micrograph averageTaW
50 nm
“optimalgranularity“
MetallObjekt
O1 O2 On• • • •
MetallObjekt
O1 O2 On• • • •
cont
rast
elevationangle 45°
Polyhead freeze-dried and rotary shadowed (30°)
13 nm
-statistical nucleation-averaging out granularity
H. Gross...
Pseudoreplica (freeze-dried coated or stained) of macromolecular complexes...SEM images
R. Hermann 1990
J. Woodward 2009
S-900 in-lens...
freeze-dried and shadowed with 1nm W or from negative staining...
Surface relief reconstruction from SEM data....
J.D. Woodward...2009
Surface relief reconstruction from SEM dataBasic’s to understand:
- principles of diffraction-based methods
- grounding by understanding only simple algebra
- visual representation & explanations
- cryo-EM & X-ray crystallography
-> crystals (3D/2D), helices, viral geometry & single particle
The context matters...
“The Art lies in the context....”
Why imaging?Nano-bio-morphology: Morphomics
Genomics: X genes and regulation of expression (35000 genes)
Proteomics: X proteins with Y variations & Z functions with i interactions (potential partners)
Metabolomics: X molecules with specific turn over pathways and products (biochemical pathway)
“All these knowledge” has to be integrated into a cellular architecture for a certain cell state at a given time and function...”
How is this all wired in a cell (molecular wiring)???
The blue-print tells us more than the sum of the single particles..
" the 3D Nano-Bio-Morphology gets into the focus of the future life-science activities
“Morphomics”: subcellular ultrastructure needs to be integrated into the cellular and tissue context => Light &Electron Microscopy
Why EM for Life Science..... but please not only Science Hollywood.....
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http://multimedia.mcb.harvard.edu/media.html
10 nm
100nm
1 nm
MolecularTEM
Objects “thin”e--transparent
CellularEM
1µ
Objects “thick”not e--transparent
EM in Life-Science: Cellular & Molecular....
Aim: The Cellular Nano-Morphology at the life-like StateIntact
biologicalSystem
Preparationfor EM
ElectronMicroscopy
Image Interpretation&
Reconstruct ion
StructureSimulation
•Micro-Biopsy•fast•controlled•physiological conditions
•freezing in ms•life-like preservation•vitrified water•no ice crystals
•selectiv dehydration•no shrinkage•no loss & displacement•antigen preservation
•projection maps•pattern recongnition•tomography•low dose
•selection•distortion•calibration•fi ltering
•autoalignment•adjustmentsignal/distortion•calibration•volume recovering
•selection•reduction•complexity•rendering•animation
Serial sections
Low temperatureembedding
Freeze-substitution
TEM (SEM):
Freezing
Sampleext ract ion: F reez ing: C r y o -
preparat ion:Image
process ing:Image
reconst ruct ion:Computer
model :
Information Transfer System (Information Transfer Function...)
“thin” section
3D Electron Microscopy
10nm
100nm
1
“thin”e--transparent => “Tomography”
(various angle views..)
“thin” => tilt series
-> virtual imagestack
1
“Thick”not e--transparent=> serial section
real section or “en-bloc”
section projections or bloc-face view
=> Image Stack
“replica” freeze fracture
“thin” section
Large Volume 3D EM methods...
K.L.Briggman&D.D.Bocks 2012;
SEM
SEMSEM
TEMS(T)EM
Block Face ImagingSection Imaging
! 3D - Data from sections....
! classical serial sectioning...-> TEM! serial sectioning (arrays) for SEM! serial sectioning in the SEM...->
! serial sectioning in the FIB/SEM...->
! tomographic view of section volume...->TEM Tomo
! serial section TEM-tomography...
Structure accessibility for SEM & TEM: serial sectioning...
50-100nm sections...
serial sections...(RT or cryo)
From serial sections to 3-D model:
High Pressure Frozen, Freeze-Substituted Paramecia, HM20 embedded, RT serial sections, TEM
Paramecia 3-D reconstruction:
Context embedded 3D models of entities of interest
! 3D - Data from sections....
Serial section array SEM imaging:K. D. Micheva, S.J. SmithNeuron 55, 2007
Can SEM replace classical TEM application for ultrastructure research?
Brain Sections (TEM vs. SEM, FIB/SEM...) TEM section on ITO glass slides - dwell time vs. S/N
6144 x 4608 pixel(1‘415‘577‘600pixel) 1.75nm/pixel
10kx; WD 2,3mmBSE(EsB Det.)SE (in-lens)
=> max speedSE: 50nsec/pixel
BSE: 400nsec/pixel
Ip=855pA45.8s/frame1,6µs/pixel
Ip=855pA23.1s/frame0,817µs/pixel
Ip=232pA1.5min/frame3.2µs/pixel
Brain Sections (TEM vs. SEM, FIB/SEM...) TEM section on ITO glass slides - dwell time vs. S/N
6144 x 4608 pixel(1‘415‘577‘600pixel) 1.75nm/pixel
10kx; WD 2,3mmBSE(EsB Det.)SE (in-lens)
=> max speedSE: 50nsec/pixel
BSE: 400nsec/pixel
Ip=855pA45.8s/frame1,6µs/pixel
Ip=855pA23.1s/frame0,817µs/pixel
Ip=232pA1.5min/frame3.2µs/pixel
Merchan_Perez 2009FIB/SEM
Beckmann Inst. TEM
SEM
Sample preparation
High-pressure Freezing
Freeze substitution & low temp. embedding
SEM tomography
Katja Kawaschinski; 2000 ; Biel et al., J Microsc 212 (2003)
e.g.cell culturemicroorganisms tissue (biopsy)plants material …
C. elegans
Soy bean plant
Cell culture on sapphire disc
+ UAc and/ or OsO4
+ Fluorescent dyes e.g. DiIC18
Determination of ROI & serial sectioning
CLSM
40x
Tissue…
FIB
SEM
Sample preparation
High-pressure Freezing
Freeze substitution & low temp. embedding
3D FIB-SEM tomography
Katja Kawaschinski; 2000 ; Biel et al., J Microsc 212 (2003)
e.g.cell culturemicroorganisms tissue (biopsy)plants material …
C. elegans
Soy bean plant
Cell culture on sapphire disc
+ UAc and/ or OsO4
+ Fluorescent dyes e.g. DiIC18
Determination of ROI & 3D imaging
CLSM
40x
Tissue…
! 3D - Data from sections....
! classical serial sectioning...-> TEM! serial sectioning (arrays) for SEM! serial sectioning in the SEM...-> W. Denk
Lit: W. Denk & H. Horstmann, 2004, PLos Biol.2, “Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure”
! serial sectioning in the FIB/SEM...-> a new way to section embedded sample (resin and cryo...)
FIB: Focussed Ion Beam - the “ion knife”
! ‚DualBeam‘: Sample illumination by electron and/or ion beams! in situ sample preparation...
SEM mode FIB mode “CrossBeam”/ “Dual Beam”
www.smt.zeiss.comOctober 20, [email protected]
Acquisition of 3D image stacks with FIB-SEM1. Deposition of protecting C-layer
2. Milling of a trench, milling current 6.5 - 13nA
3. Polish the cross section, milling current 1.5nA
4. Imaging with SEM (ESB)
5. cut again a slice away with ion beam
6. repeat 4.-5. for acquisition of a 3D serial section stack (fully automatized)
Ion-beam
e-beam
Jason Mercer/Ari Helenisu IBC and Miriam Droste/ Roger Wepf EMEZ - Anreas Schertel Zeiss
Acquisition of 3D stack by FIB / SEM
Dr. Miriam Droste
Acquisition of 3D stack by FIB / SEM
FIB-SEM: ROI extraction of a lamella for HR-TEM Tomography...
Roger Wepf/; Miriam Lucas; Falk Lucas, Maja Günthert...
LM#–#Dark#field
FIB/SEM vs section: limited volume by FIB/SEM....
2kV - BSE 2kV - BSE
Can we look at larger sample area’s by SEM?
Two alternatives:
- in-situ microtome (3View or Denkatome - computer controlled)
- array tomography (CAT - correlative/computer controlled)
Large Volume 3D EM methods...
K.L.Briggman&D.D.Bocks 2012;
SEM
SEMSEM
TEMS(T)EM
- array tomography (CAT - correlative/computer controlled)
“3View”
SEM
Sample preparation
High-pressure Freezing
Freeze substitution & low temp. embedding
SEM tomography
Katja Kawaschinski; 2000 ; Biel et al., J Microsc 212 (2003)
e.g.cell culturemicroorganisms tissue (biopsy)plants material …
C. elegans
Soy bean plant
Cell culture on sapphire disc
+ UAc and/ or OsO4
+ Fluorescent dyes e.g. DiIC18
Determination of ROI & serial sectioning
CLSM
40x
Tissue…
3D data with an in situ ultramicrotome.....(Denkatome....Denk&Horstmann 2004 PLOS Vol 2)
May be combined with CLSM of pre-embedding antibody labeling, or diffusible dyes....- fast for large volumes- destructive- large amount of heavy metal needed- e-beam induced hardening during operation Gatan 3View....
Tissue…
3D data with an in situ ultramicrotome.....(Denkatome....Denk&Horstmann 2004 PLOS Vol 2)
May be combined with CLSM of pre-embedding antibody labeling, or diffusible dyes....- fast for large volumes- destructive- large amount of heavy metal needed- e-beam induced hardening during operation
3D data with an in situ ultramicrotome.....(Denkatome....Denk&Horstmann 2004 PLOS Vol 2)
May be combined with CLSM of pre-embedding antibody labeling, or diffusible dyes....- fast for large volumes- destructive- large amount of heavy metal needed- e-beam induced hardening during operation
Tissue…
Liver tissue...
Mitochondria in 3D
Ultra thin section imaging by SEM
SEM section imaging for ultrastructure (TEM quality....)
LM (Histo, FLM, DF, DIC...)
SEM (SE, BSE)
- highly flexible for LM modes- not limited in size and orientation- no Cu-bar covering “the most interesting region”- immunolabeling possible...
! Large number ultra-thin section imaging easier in SEM....
Wilke et al,; 2008TEM (Grid...)
SEM conquers TEM ultrastructure domain (Life-Science)
! 3D LM/SEM - Data from sections...Array Tomography
Serial section array SEM imaging:K. D. Micheva, S.J. SmithNeuron 55, 2007
1. Chemical Fixation2. Dehydration3. Embedding4. Serial sections
5. Post-embedding labeling6. Multilabeling...7. Histo or SEM-> Au-BSE localisation???
Correlative Microscopy 2 - Array Tomography: - 60 Sections (80nm)- 310µm x 230µm; 5nm pixelsize; 4µsec dwell time...- Matrix of 4 x 3 images each 16384 x 16384pixels
=> 3’221’225’472 pixel per ROI ! => Acquisition time is per ROI 4h 9min!
310µm x 230µm x 4,8µmGemini 1530LM Stack: 440MB
SEM Stack: 197 GBCloud Microscopy: www.cubicice.de
Array Tomography & Immunolocalisation (lipids): - primary antibody against Glucosyl-Ceramid 3; secondary antibody Cy3
Correlative Microscopy 2 - Array Tomography: - 60 Sections (80nm)- 310µm x 230µm; 5nm pixelsize; 4µsec dwell time...- Matrix of 4 x 3 images each 16384 x 16384pixels
=> 3’221’225’472 pixel per ROI ! => Acquisition time is per ROI 4h 9min!
310µm x 230µm x 4,8µmGemini 1530LM Stack: 440MB
SEM Stack: 197 GB
! 3D - Data from sections in TEM....
! tomographic view of section volume...->TEM Tomo
! serial section TEM-tomography...
TEM Tomography: multilamellar bodies in the Stratum Granulosum..
•Stratum Corneum lipids are synthesised in the TGN (GluCer) and exported in Multivesicular lamellar bodies into the intercellular space (Cer)...
80nm HM20 sectionfrom a sample freeze-substituted 1999
Resin embedded samplesare a “Storage” device for “morphomic data”
-> “Data block” &" “Data slices”
Reinvestigated 2002 by TEM Tomography...-> membrane visibility!
Membrane Visibility in TEM sections - basic morphology
80nm HM20 sectionfrom a sample freeze-substituted 1999-> “Data block” &" “Data slices”
A “Storage”of morphomic data
Tilt: -60deg to +60deg
John O‘Brien; © 1991 The New Yorker Magazine
3-D reconstruction of Golgi-TGN from TEM Tomography:
http://bio3d.colorado.edu/pubs/Golgi/GolgiAnalysis.htmlLadinsky et. al. (1999). Golgi structure in three dimensions: Functional insights from the NRK cell. J. Cell Biol., 144: 1135-1149.
3-D reconstruction of whole cells (B.Marsh):
from 46 and 27 sections- each reconstructed from a TEM Tomogram...-> 3D statistical data
Expedited approaches to whole cell electron tomography andorganelle mark-up in situ in high-pressure frozen pancreatic isletsAndrew B. Noske a,b, Adam J. Costin a,1, Garry P. Morgan a,1, Brad J. Marsh a,b,c,* JSB 2007
Summary: 3D tissue imaging....
EM-Holography? ... mainly for solid state materials not yet successful in LS
“thin” section
3D Electron Microscopy
10nm
100nm
1 nm
“thin”e--transparent => “Tomography”
(various angle views..)
1µ
“Thick”not e--transparent=> serial section
real section or “en-bloc”
section projections or bloc-face view
=> Image Stack
The LM/SEM (FIB) world
Cryo-SEM
The LM/TEM world
“thin” => tilt series-> virtual image
stack
=> TEM “Tomo”
serial section LM/SEM
How to Read 3D EM data...! see. Lit: Saibil, HR (2007) How to read papers on three-
dimensional structure determination by electron microscopy. in Evaluating techniques in biomedical research, Cell Press
Some further reading on 3D EM data...
Hoffpauir, Pope and Spirou (2007); “Serial sectioning and electron microscopy of large tissue volumes for 3D analysis and reconstruction: a case study of the caly of Held, Nature Protocols; Vol.2 No.1
Some further reading on 3D EM data...
Golas, M. M., C. Boehm, B. Sander, K. Effenberger, M. Brecht, H. Stark and H. U. Goeringer: Snapshots of the RNA editing machine in trypanosomes captured at different assembly stages in vivo. EMBO Journal 28, 766-778 (2009)
comprehensible “Nano-cosmos”
in its natural context Thanks for your attention ...