Ondrej L Shanel, Ph.D. Transmision electron microscopy - TEM • TEM mode - Image of an illuminated sample is magnified onto a camera • STEM Mode - Focused Beam scanning over the sample -> processed signal creates an image Accelerator Gun Deflectors Condenser Lens 4 Condenser Lens Condensor aperture Objective len Image Deflectors/Stigmator Selective Area/DiffractiorT^ aperture Diffraction rrftSftnediate Lens Projective Lens 1 +2 Projection Chamber- "ITEC Condensor Deflectors/Stigmator s Sample/ Sample holder Sample stage ■ ui ■ UI ■ III Camer Data Storage Transmision electron microscopy - Optical modes Gun Filament Condensor1 Condensor 2 Condensor aperture Upper part of Objective lens flower part of Objective ^ampl leififeck focal plane Diffraction lens Intermediate lens P1 lens P2 lens Camera/Detector \-» Sample- £2 _- I ■ \ : TEM - Imaging TEM Diffraction STEM Imaging Transmitted primary electrons Wavefronts representing incoming electron beam Incident electrons © © © ^incW ^inoQi inc Sample i/>s(r') Ef,qf Resulting wavefront Specimer atom Inelastically scattered electron Elasticallv Unscattered scattered electron electron Dr. Konecnä - CPO VUT 2022/2023 Elastic scattering on a signle atom Final electron wave function after the interaction with an atom L i/>s(0 = ^inc(r)+/eO/) exp(i q • r) Scattering cross section: a = 2ni n 00 J 7o ^0 (qr) \ 1 — exp j 0(r)cL J me A 2nh2 r dr For acquiring an image, we propagate ips(x) through an electron-optical system: Wtor OC IFT-H^sCQ) TF(Q)}|: Dr. Konecna -CPO VUT 2022/2023 Elastic scattering on a signle atom Final electron wave function after the interaction with an atom: L i/>s(0 = ^inc(r)+/eO/) exp(i q • r) Scattering cross section: a = 2ni n CO J 7o ^0 (gr) \ 1 — exp j 0(r)cL me A 2nh2 r dr Calculation for ipinc oc exp(i 2nz/A) 200 keV electrons (Kirkland; Advanced computing in EM) Si Cu Au U Dr. Konecna -CPO VUT 2022/2023 Transfer of Image through the optical system inc Sample A(x,y) - absorbtion inc(r) = 1 (parallel illumination) Exit Wave 0s(r) = tfcnc(r)[l + e(r) + i«jo(r)] t/^/p (?) = FT{ips(r)} ^bfP (?) = 5(q) + £(q) + iO(q) Aberrations addition W(q) = - (C30q*AS + C10g A) tfVP,a> (?) = 5(9) + E{q)e-iw^ + M>(qf)c-^&) Optical Intensity at Image Plane C3 o - spherical aberration C± o - defocus W = \ipm(Rdet)\2 = FTifjbfPiabFTipbfpab Optical Intensity at Image Plane with Dumping Envelope (System imperefections) KR) = \*l>m(Rdet)\2 = Et * EsEdEu{l - 2 AU> A/) Fs(q') - spatial coherency Es(q') =e~n2^3'°x2q'3~c^°q')2a2/ln2 Ed(q') - drift impact Eu(q')- vibration dumping Observed Intensity on PC CTF is not seen directly on our PC! Intensityob(r') = irn + idc + cf IFT — j> 06 s a c 8 04 IB E L_ O 2! ft * ift"1 ctfoptical(0 - defocus Practical hint: Higher defocus promote contrast in low frequecies (lost at higher) Work in Parallel illumination Intenzita(r')det TEM - phase contrast - Influence of Defocus CTF*sqrt(DQE) Parallel illumination Defocus Onm Defocus -500nm 1.10E-10 6.00E-11 l.OOE-ll h ■D 01 -0,2 .a nj E o -0,4 Z 10urad illumination Defocus Onm Defocus -500nm TEM - phase contrast III -0.75 nm -1.5[im -3.0 [am o s S£2><=EEITEE<= SPA particle with different defocus https://cryoem101 .org/chapter-5/ TEM imaging - Influence of Cond Aperture • Definition of illuminating area + convergent angle Intenzita(4,)det=£'t(^')£'sW')£'dW,)£'uW,) ■ Intenzita(q') • Spatial dumping envelope Es(q') = e(C3A2l'3-Ci,oQl2af/ln2 A I j 4» 1-► Sample <- at is convergent angle of illumination c3,o - spherical aberration C10 - defocus • Practical hint: • Work as close to parallel illumination - feel free to use Gun lens or spot size to manage your dose 1 Intenzita(r')det TEM imaging - Influence of Cond Aperture CTF*sqrt(DQE) 11urad illumination Parallel illumination 1 -l Spatial frequency [m] ^CEITEC 17 TEM imaging - Influence of Obj Aperture 42>CEITEC Influence of Obj Aperture TEM imaging - Influence of Obj Aperture TEM imaging - Influence of SA Aperture • Limiting FOV(r) • No advantage for TEM imaging tf'outCr) = 1 + e(r) + icp(r) TEM imaging - Influence of Detector • Critical for TEM imaging Intensityob(K) = Im + idc + CF IFT FT ^oiss *e * IFT" )^dqe(^) NTF(tf) /r-r. - camera read-out noise dark current CF - Conversion factor - how much primar electrons are count as 1 signal Oe - number of primary electron on a pixel (MTF)2 DQE = = „how well camera can trasfer details" Power Spectrum NTF - Noise Transfer Function (related to non-elastic scattering of the sample Practical hint: Make your Dark current calibration each 2 weeks or monthly Check your camera cooling stability Do not overexpose your camera Intenzita(f')det TEM imaging - Influence of Detector CTF*sqrt(DQE) Direct Electron Camera Scintilator Based Camei -l Spatial frequency [m] ££2><=EEITEE<= Diffraction imaging - Influence of SA Aperture • SA aperture selecting Sample region for Diffraction • SA selection vs Nano Beam Diffraction No fringes in SA image Illuminating whole sample ip0(r) = 1 RISK OF CAMERA DAMAGE!!! Intensity^(r") = Im + idc + CF IFT FT Foiss f • IFT"1 ctfüptical(^' NTF(q') Irn - camera read-out noise Idc - dark current CF - Conversion factor - how much primar electrons are count as 1 signal Oe - number of primary electron on a pixel DQE = {MT FY = „how well camera can trasfer details" Power Spectrum NTF - Noise Transfer Function (related to non-elastic scattering of the sample Practical hint: Shield your Zero order diffraction peak to avoid damaging camera CL as magnification IntenzitaCqOdet Diffraction imaging - Influence of Cond Aperture • Non-critical for SAED - defining mainly illuminated FOV • Critical for CBED • Definition of Ronchigram size 02aPe7t^ Sample <- Droncht (r) - s'ze of ronchigram in reciprocal space SA*pertu Dap (f) - size of C2 aperture M / - focal lenght of condensor <— • Practical hint Allways condensor stigmate on Ronchigram Conclusion TEM imaging providing atomic resolution Knowledge of your system setup is crucial for image interpretation (further processing) S^CEITEC