[{"data":1,"prerenderedAt":1169},["ShallowReactive",2],{"mdc--qtmx24-key":3},{"data":4,"body":5},{},{"type":6,"children":7},"root",[8,17,45,49,55,60,89,101,130,135,147,158,161,167,172,181,193,196,203,208,226,231,236,241,259,264,272,275,281,285,310,315,320,325,335,340,363,366,372,377,380,386,404,407,413,436,445,448,454,487,492,505,508,514,519,522,528,551,555,565,570,578,581,587,600,604,613,618,627,632,640,643,649,654,657,663,676,679,685,690,708,713,767,772,777,782,787,792,797,800,806,811,821,826,864,869,877,880,886,891,896,899,905,923,928,933,936,942,955,958,964,977,982,990,993,999,1004,1009,1042,1047,1057,1062,1067,1077,1080,1086,1091,1096,1119,1124,1129,1137,1140,1146,1157,1164],{"type":9,"tag":10,"props":11,"children":13},"element","h1",{"id":12},"lecture-8-video-4-cryo-em-image-formation-contrast-fourier-space",[14],{"type":15,"value":16},"text","🎥 Lecture 8 Video 4 — Cryo-EM Image Formation, Contrast & Fourier Space",{"type":9,"tag":18,"props":19,"children":20},"p",{},[21,23,29,31,36,38,43],{"type":15,"value":22},"This lecture explains ",{"type":9,"tag":24,"props":25,"children":26},"strong",{},[27],{"type":15,"value":28},"how electron microscope images are formed",{"type":15,"value":30},", why ",{"type":9,"tag":24,"props":32,"children":33},{},[34],{"type":15,"value":35},"contrast is difficult in cryo-EM",{"type":15,"value":37},", and how ",{"type":9,"tag":24,"props":39,"children":40},{},[41],{"type":15,"value":42},"Fourier transforms help us reconstruct 3D structures",{"type":15,"value":44},".",{"type":9,"tag":46,"props":47,"children":48},"hr",{},[],{"type":9,"tag":10,"props":50,"children":52},{"id":51},"_1-electron-waveparticle-duality-image-formation",[53],{"type":15,"value":54},"⚡ 1. Electron Wave–Particle Duality & Image Formation",{"type":9,"tag":18,"props":56,"children":57},{},[58],{"type":15,"value":59},"Electrons behave both like:",{"type":9,"tag":61,"props":62,"children":63},"ul",{},[64,77],{"type":9,"tag":65,"props":66,"children":67},"li",{},[68,70,75],{"type":15,"value":69},"🔵 ",{"type":9,"tag":24,"props":71,"children":72},{},[73],{"type":15,"value":74},"Particles",{"type":15,"value":76}," → detected as individual hits on detectors",{"type":9,"tag":65,"props":78,"children":79},{},[80,82,87],{"type":15,"value":81},"🌊 ",{"type":9,"tag":24,"props":83,"children":84},{},[85],{"type":15,"value":86},"Waves",{"type":15,"value":88}," → interfere and produce contrast patterns",{"type":9,"tag":18,"props":90,"children":91},{},[92,94,99],{"type":15,"value":93},"An electron beam entering the microscope is almost like a ",{"type":9,"tag":24,"props":95,"children":96},{},[97],{"type":15,"value":98},"plane wave",{"type":15,"value":100}," that:",{"type":9,"tag":102,"props":103,"children":104},"ol",{},[105,110,115,120],{"type":9,"tag":65,"props":106,"children":107},{},[108],{"type":15,"value":109},"Interacts with atoms in the specimen",{"type":9,"tag":65,"props":111,"children":112},{},[113],{"type":15,"value":114},"Gets scattered or transmitted",{"type":9,"tag":65,"props":116,"children":117},{},[118],{"type":15,"value":119},"Recombines in the image plane",{"type":9,"tag":65,"props":121,"children":122},{},[123,125],{"type":15,"value":124},"Produces an ",{"type":9,"tag":24,"props":126,"children":127},{},[128],{"type":15,"value":129},"interference pattern = image",{"type":9,"tag":18,"props":131,"children":132},{},[133],{"type":15,"value":134},"Important fact:",{"type":9,"tag":18,"props":136,"children":137},{},[138,140,145],{"type":15,"value":139},"👉 ",{"type":9,"tag":24,"props":141,"children":142},{},[143],{"type":15,"value":144},"Most electrons are NOT scattered — they just pass through.",{"type":15,"value":146},"\nOnly a small fraction interacts and contributes to image formation.",{"type":9,"tag":18,"props":148,"children":149},{},[150,152,157],{"type":15,"value":151},"This is one major reason why ",{"type":9,"tag":24,"props":153,"children":154},{},[155],{"type":15,"value":156},"cryo-EM images are noisy and low contrast",{"type":15,"value":44},{"type":9,"tag":46,"props":159,"children":160},{},[],{"type":9,"tag":10,"props":162,"children":164},{"id":163},"_2-what-is-contrast-in-electron-microscopy",[165],{"type":15,"value":166},"🎨 2. What is Contrast in Electron Microscopy?",{"type":9,"tag":18,"props":168,"children":169},{},[170],{"type":15,"value":171},"Contrast simply means:",{"type":9,"tag":173,"props":174,"children":175},"blockquote",{},[176],{"type":9,"tag":18,"props":177,"children":178},{},[179],{"type":15,"value":180},"Difference between bright and dark areas that allows us to distinguish structures.",{"type":9,"tag":18,"props":182,"children":183},{},[184,186,191],{"type":15,"value":185},"In cryo-EM there are ",{"type":9,"tag":24,"props":187,"children":188},{},[189],{"type":15,"value":190},"two main contrast mechanisms",{"type":15,"value":192},":",{"type":9,"tag":46,"props":194,"children":195},{},[],{"type":9,"tag":197,"props":198,"children":200},"h2",{"id":199},"amplitude-contrast-particle-view",[201],{"type":15,"value":202},"🔴 Amplitude Contrast (Particle view)",{"type":9,"tag":18,"props":204,"children":205},{},[206],{"type":15,"value":207},"This occurs when:",{"type":9,"tag":61,"props":209,"children":210},{},[211,221],{"type":9,"tag":65,"props":212,"children":213},{},[214,216],{"type":15,"value":215},"Some electrons are ",{"type":9,"tag":24,"props":217,"children":218},{},[219],{"type":15,"value":220},"absorbed or scattered away",{"type":9,"tag":65,"props":222,"children":223},{},[224],{"type":15,"value":225},"Fewer electrons reach the detector behind dense objects",{"type":9,"tag":18,"props":227,"children":228},{},[229],{"type":15,"value":230},"Result:",{"type":9,"tag":18,"props":232,"children":233},{},[234],{"type":15,"value":235},"➡ Darker regions where electrons were removed.",{"type":9,"tag":18,"props":237,"children":238},{},[239],{"type":15,"value":240},"Mechanism:",{"type":9,"tag":61,"props":242,"children":243},{},[244,249,254],{"type":9,"tag":65,"props":245,"children":246},{},[247],{"type":15,"value":248},"High-angle scattering",{"type":9,"tag":65,"props":250,"children":251},{},[252],{"type":15,"value":253},"Absorption",{"type":9,"tag":65,"props":255,"children":256},{},[257],{"type":15,"value":258},"Electron-dense material blocks beam",{"type":9,"tag":18,"props":260,"children":261},{},[262],{"type":15,"value":263},"You can imagine:",{"type":9,"tag":173,"props":265,"children":266},{},[267],{"type":9,"tag":18,"props":268,"children":269},{},[270],{"type":15,"value":271},"“Electron shadow” behind dense objects.",{"type":9,"tag":46,"props":273,"children":274},{},[],{"type":9,"tag":197,"props":276,"children":278},{"id":277},"phase-contrast-wave-view",[279],{"type":15,"value":280},"🟣 Phase Contrast (Wave view)",{"type":9,"tag":18,"props":282,"children":283},{},[284],{"type":15,"value":207},{"type":9,"tag":61,"props":286,"children":287},{},[288,298],{"type":9,"tag":65,"props":289,"children":290},{},[291,293],{"type":15,"value":292},"Electrons are ",{"type":9,"tag":24,"props":294,"children":295},{},[296],{"type":15,"value":297},"not removed",{"type":9,"tag":65,"props":299,"children":300},{},[301,303,308],{"type":15,"value":302},"Their ",{"type":9,"tag":24,"props":304,"children":305},{},[306],{"type":15,"value":307},"phase (timing of wave oscillation)",{"type":15,"value":309}," changes.",{"type":9,"tag":18,"props":311,"children":312},{},[313],{"type":15,"value":314},"Key idea:",{"type":9,"tag":18,"props":316,"children":317},{},[318],{"type":15,"value":319},"➡ The wave shifts slightly in position → interference creates contrast.",{"type":9,"tag":18,"props":321,"children":322},{},[323],{"type":15,"value":324},"In cryo-EM:",{"type":9,"tag":18,"props":326,"children":327},{},[328,330],{"type":15,"value":329},"⭐ ",{"type":9,"tag":24,"props":331,"children":332},{},[333],{"type":15,"value":334},"Phase contrast is the dominant mechanism.",{"type":9,"tag":18,"props":336,"children":337},{},[338],{"type":15,"value":339},"This is because:",{"type":9,"tag":61,"props":341,"children":342},{},[343,353,358],{"type":9,"tag":65,"props":344,"children":345},{},[346,348],{"type":15,"value":347},"Proteins and water have ",{"type":9,"tag":24,"props":349,"children":350},{},[351],{"type":15,"value":352},"similar electron densities",{"type":9,"tag":65,"props":354,"children":355},{},[356],{"type":15,"value":357},"So amplitude contrast is weak",{"type":9,"tag":65,"props":359,"children":360},{},[361],{"type":15,"value":362},"Phase shifts carry most structural information.",{"type":9,"tag":46,"props":364,"children":365},{},[],{"type":9,"tag":10,"props":367,"children":369},{"id":368},"_3-types-of-electron-scattering",[370],{"type":15,"value":371},"💥 3. Types of Electron Scattering",{"type":9,"tag":18,"props":373,"children":374},{},[375],{"type":15,"value":376},"When electrons hit atoms, three outcomes are possible:",{"type":9,"tag":46,"props":378,"children":379},{},[],{"type":9,"tag":197,"props":381,"children":383},{"id":382},"_1-no-scattering-transmission",[384],{"type":15,"value":385},"✅ 1. No scattering (Transmission)",{"type":9,"tag":61,"props":387,"children":388},{},[389,394,399],{"type":9,"tag":65,"props":390,"children":391},{},[392],{"type":15,"value":393},"Electron passes straight through",{"type":9,"tag":65,"props":395,"children":396},{},[397],{"type":15,"value":398},"No energy loss",{"type":9,"tag":65,"props":400,"children":401},{},[402],{"type":15,"value":403},"Does NOT contribute much to image contrast",{"type":9,"tag":46,"props":405,"children":406},{},[],{"type":9,"tag":197,"props":408,"children":410},{"id":409},"_2-elastic-scattering-very-important",[411],{"type":15,"value":412},"⭐ 2. Elastic scattering (Very important!)",{"type":9,"tag":61,"props":414,"children":415},{},[416,426,431],{"type":9,"tag":65,"props":417,"children":418},{},[419,421],{"type":15,"value":420},"Electron is deflected but ",{"type":9,"tag":24,"props":422,"children":423},{},[424],{"type":15,"value":425},"keeps its energy",{"type":9,"tag":65,"props":427,"children":428},{},[429],{"type":15,"value":430},"Produces phase shifts",{"type":9,"tag":65,"props":432,"children":433},{},[434],{"type":15,"value":435},"Forms the useful structural signal",{"type":9,"tag":18,"props":437,"children":438},{},[439,440],{"type":15,"value":139},{"type":9,"tag":24,"props":441,"children":442},{},[443],{"type":15,"value":444},"Elastic scattering is what builds the image.",{"type":9,"tag":46,"props":446,"children":447},{},[],{"type":9,"tag":197,"props":449,"children":451},{"id":450},"️-3-inelastic-scattering-bad",[452],{"type":15,"value":453},"⚠️ 3. Inelastic scattering (Bad!)",{"type":9,"tag":61,"props":455,"children":456},{},[457,462,467,477],{"type":9,"tag":65,"props":458,"children":459},{},[460],{"type":15,"value":461},"Electron loses energy",{"type":9,"tag":65,"props":463,"children":464},{},[465],{"type":15,"value":466},"Can eject secondary electrons",{"type":9,"tag":65,"props":468,"children":469},{},[470,472],{"type":15,"value":471},"Causes ",{"type":9,"tag":24,"props":473,"children":474},{},[475],{"type":15,"value":476},"radiation damage",{"type":9,"tag":65,"props":478,"children":479},{},[480,482],{"type":15,"value":481},"Adds ",{"type":9,"tag":24,"props":483,"children":484},{},[485],{"type":15,"value":486},"noise",{"type":9,"tag":18,"props":488,"children":489},{},[490],{"type":15,"value":491},"Therefore:",{"type":9,"tag":173,"props":493,"children":494},{},[495],{"type":9,"tag":18,"props":496,"children":497},{},[498,500],{"type":15,"value":499},"Cryo-EM tries to ",{"type":9,"tag":24,"props":501,"children":502},{},[503],{"type":15,"value":504},"maximize elastic scattering and minimize inelastic scattering.",{"type":9,"tag":46,"props":506,"children":507},{},[],{"type":9,"tag":10,"props":509,"children":511},{"id":510},"_4-negative-stain-vs-cryo-em-contrast",[512],{"type":15,"value":513},"🧪 4. Negative Stain vs Cryo-EM Contrast",{"type":9,"tag":18,"props":515,"children":516},{},[517],{"type":15,"value":518},"This lecture gives a very important conceptual comparison.",{"type":9,"tag":46,"props":520,"children":521},{},[],{"type":9,"tag":197,"props":523,"children":525},{"id":524},"negative-stain-em",[526],{"type":15,"value":527},"🟤 Negative Stain EM",{"type":9,"tag":61,"props":529,"children":530},{},[531,536,541],{"type":9,"tag":65,"props":532,"children":533},{},[534],{"type":15,"value":535},"Heavy metal stain surrounds protein",{"type":9,"tag":65,"props":537,"children":538},{},[539],{"type":15,"value":540},"Huge electron density difference",{"type":9,"tag":65,"props":542,"children":543},{},[544,546],{"type":15,"value":545},"Strong ",{"type":9,"tag":24,"props":547,"children":548},{},[549],{"type":15,"value":550},"amplitude contrast",{"type":9,"tag":18,"props":552,"children":553},{},[554],{"type":15,"value":230},{"type":9,"tag":18,"props":556,"children":557},{},[558,560],{"type":15,"value":559},"➡ Protein appears ",{"type":9,"tag":24,"props":561,"children":562},{},[563],{"type":15,"value":564},"white in dark background",{"type":9,"tag":18,"props":566,"children":567},{},[568],{"type":15,"value":569},"Why?",{"type":9,"tag":61,"props":571,"children":572},{},[573],{"type":9,"tag":65,"props":574,"children":575},{},[576],{"type":15,"value":577},"Heavy stain scatters electrons strongly.",{"type":9,"tag":46,"props":579,"children":580},{},[],{"type":9,"tag":197,"props":582,"children":584},{"id":583},"️-cryo-em",[585],{"type":15,"value":586},"❄️ Cryo-EM",{"type":9,"tag":61,"props":588,"children":589},{},[590,595],{"type":9,"tag":65,"props":591,"children":592},{},[593],{"type":15,"value":594},"Protein embedded in vitreous ice (water)",{"type":9,"tag":65,"props":596,"children":597},{},[598],{"type":15,"value":599},"Small density difference",{"type":9,"tag":18,"props":601,"children":602},{},[603],{"type":15,"value":230},{"type":9,"tag":18,"props":605,"children":606},{},[607,608],{"type":15,"value":559},{"type":9,"tag":24,"props":609,"children":610},{},[611],{"type":15,"value":612},"dark on grey background",{"type":9,"tag":18,"props":614,"children":615},{},[616],{"type":15,"value":617},"Main contrast source:",{"type":9,"tag":18,"props":619,"children":620},{},[621,622],{"type":15,"value":329},{"type":9,"tag":24,"props":623,"children":624},{},[625],{"type":15,"value":626},"Phase contrast (not amplitude).",{"type":9,"tag":18,"props":628,"children":629},{},[630],{"type":15,"value":631},"This explains:",{"type":9,"tag":173,"props":633,"children":634},{},[635],{"type":9,"tag":18,"props":636,"children":637},{},[638],{"type":15,"value":639},"Why cryo-EM images look noisy and faint.",{"type":9,"tag":46,"props":641,"children":642},{},[],{"type":9,"tag":10,"props":644,"children":646},{"id":645},"_5-real-space-vs-fourier-space",[647],{"type":15,"value":648},"🧠 5. Real Space vs Fourier Space",{"type":9,"tag":18,"props":650,"children":651},{},[652],{"type":15,"value":653},"A fundamental concept in structural biology imaging.",{"type":9,"tag":46,"props":655,"children":656},{},[],{"type":9,"tag":197,"props":658,"children":660},{"id":659},"️-real-space",[661],{"type":15,"value":662},"🖼️ Real Space",{"type":9,"tag":61,"props":664,"children":665},{},[666,671],{"type":9,"tag":65,"props":667,"children":668},{},[669],{"type":15,"value":670},"What we normally see",{"type":9,"tag":65,"props":672,"children":673},{},[674],{"type":15,"value":675},"The actual particle image (micrograph)",{"type":9,"tag":46,"props":677,"children":678},{},[],{"type":9,"tag":197,"props":680,"children":682},{"id":681},"fourier-space-power-spectrum",[683],{"type":15,"value":684},"🌐 Fourier Space (Power Spectrum)",{"type":9,"tag":18,"props":686,"children":687},{},[688],{"type":15,"value":689},"After Fourier transform:",{"type":9,"tag":61,"props":691,"children":692},{},[693,703],{"type":9,"tag":65,"props":694,"children":695},{},[696,698],{"type":15,"value":697},"Image becomes ",{"type":9,"tag":24,"props":699,"children":700},{},[701],{"type":15,"value":702},"concentric rings",{"type":9,"tag":65,"props":704,"children":705},{},[706],{"type":15,"value":707},"Represents spatial frequency information",{"type":9,"tag":18,"props":709,"children":710},{},[711],{"type":15,"value":712},"Interpretation:",{"type":9,"tag":714,"props":715,"children":716},"table",{},[717,736],{"type":9,"tag":718,"props":719,"children":720},"thead",{},[721],{"type":9,"tag":722,"props":723,"children":724},"tr",{},[725,731],{"type":9,"tag":726,"props":727,"children":728},"th",{},[729],{"type":15,"value":730},"Region",{"type":9,"tag":726,"props":732,"children":733},{},[734],{"type":15,"value":735},"Meaning",{"type":9,"tag":737,"props":738,"children":739},"tbody",{},[740,754],{"type":9,"tag":722,"props":741,"children":742},{},[743,749],{"type":9,"tag":744,"props":745,"children":746},"td",{},[747],{"type":15,"value":748},"Center",{"type":9,"tag":744,"props":750,"children":751},{},[752],{"type":15,"value":753},"Low spatial frequencies → overall shape",{"type":9,"tag":722,"props":755,"children":756},{},[757,762],{"type":9,"tag":744,"props":758,"children":759},{},[760],{"type":15,"value":761},"Outer rings",{"type":9,"tag":744,"props":763,"children":764},{},[765],{"type":15,"value":766},"High spatial frequencies → fine atomic details",{"type":9,"tag":18,"props":768,"children":769},{},[770],{"type":15,"value":771},"Low frequencies help:",{"type":9,"tag":18,"props":773,"children":774},{},[775],{"type":15,"value":776},"✅ Particle detection\n✅ Alignment",{"type":9,"tag":18,"props":778,"children":779},{},[780],{"type":15,"value":781},"High frequencies help:",{"type":9,"tag":18,"props":783,"children":784},{},[785],{"type":15,"value":786},"⭐ Atomic resolution reconstruction",{"type":9,"tag":18,"props":788,"children":789},{},[790],{"type":15,"value":791},"But:",{"type":9,"tag":18,"props":793,"children":794},{},[795],{"type":15,"value":796},"⚠️ Also contain more noise.",{"type":9,"tag":46,"props":798,"children":799},{},[],{"type":9,"tag":10,"props":801,"children":803},{"id":802},"️-6-why-use-fourier-transforms",[804],{"type":15,"value":805},"⚙️ 6. Why Use Fourier Transforms?",{"type":9,"tag":18,"props":807,"children":808},{},[809],{"type":15,"value":810},"Because they make image processing:",{"type":9,"tag":18,"props":812,"children":813},{},[814,816],{"type":15,"value":815},"🚀 ",{"type":9,"tag":24,"props":817,"children":818},{},[819],{"type":15,"value":820},"Much faster computationally.",{"type":9,"tag":18,"props":822,"children":823},{},[824],{"type":15,"value":825},"Key uses:",{"type":9,"tag":61,"props":827,"children":828},{},[829,834,839,844,849,854,859],{"type":9,"tag":65,"props":830,"children":831},{},[832],{"type":15,"value":833},"Resolution estimation",{"type":9,"tag":65,"props":835,"children":836},{},[837],{"type":15,"value":838},"Contrast Transfer Function (CTF) fitting",{"type":9,"tag":65,"props":840,"children":841},{},[842],{"type":15,"value":843},"Defocus determination",{"type":9,"tag":65,"props":845,"children":846},{},[847],{"type":15,"value":848},"Filtering (noise removal)",{"type":9,"tag":65,"props":850,"children":851},{},[852],{"type":15,"value":853},"Particle alignment",{"type":9,"tag":65,"props":855,"children":856},{},[857],{"type":15,"value":858},"Correlation analysis",{"type":9,"tag":65,"props":860,"children":861},{},[862],{"type":15,"value":863},"3D reconstruction",{"type":9,"tag":18,"props":865,"children":866},{},[867],{"type":15,"value":868},"Fourier transforms allow:",{"type":9,"tag":173,"props":870,"children":871},{},[872],{"type":9,"tag":18,"props":873,"children":874},{},[875],{"type":15,"value":876},"Moving between real space ↔ frequency space to manipulate information efficiently.",{"type":9,"tag":46,"props":878,"children":879},{},[],{"type":9,"tag":10,"props":881,"children":883},{"id":882},"️-7-filtering-in-fourier-space",[884],{"type":15,"value":885},"🎛️ 7. Filtering in Fourier Space",{"type":9,"tag":18,"props":887,"children":888},{},[889],{"type":15,"value":890},"Very powerful trick in cryo-EM.",{"type":9,"tag":18,"props":892,"children":893},{},[894],{"type":15,"value":895},"Types:",{"type":9,"tag":46,"props":897,"children":898},{},[],{"type":9,"tag":197,"props":900,"children":902},{"id":901},"low-pass-filter",[903],{"type":15,"value":904},"🔵 Low-pass filter",{"type":9,"tag":61,"props":906,"children":907},{},[908,913,918],{"type":9,"tag":65,"props":909,"children":910},{},[911],{"type":15,"value":912},"Removes high frequencies",{"type":9,"tag":65,"props":914,"children":915},{},[916],{"type":15,"value":917},"Keeps overall shape",{"type":9,"tag":65,"props":919,"children":920},{},[921],{"type":15,"value":922},"Improves contrast",{"type":9,"tag":18,"props":924,"children":925},{},[926],{"type":15,"value":927},"Used for:",{"type":9,"tag":18,"props":929,"children":930},{},[931],{"type":15,"value":932},"➡ Particle picking\n➡ Alignment",{"type":9,"tag":46,"props":934,"children":935},{},[],{"type":9,"tag":197,"props":937,"children":939},{"id":938},"high-pass-filter",[940],{"type":15,"value":941},"🔴 High-pass filter",{"type":9,"tag":61,"props":943,"children":944},{},[945,950],{"type":9,"tag":65,"props":946,"children":947},{},[948],{"type":15,"value":949},"Removes low frequencies",{"type":9,"tag":65,"props":951,"children":952},{},[953],{"type":15,"value":954},"Enhances edges / fine details",{"type":9,"tag":46,"props":956,"children":957},{},[],{"type":9,"tag":197,"props":959,"children":961},{"id":960},"band-pass-filter",[962],{"type":15,"value":963},"🟢 Band-pass filter",{"type":9,"tag":61,"props":965,"children":966},{},[967,972],{"type":9,"tag":65,"props":968,"children":969},{},[970],{"type":15,"value":971},"Removes both very low and very high frequencies",{"type":9,"tag":65,"props":973,"children":974},{},[975],{"type":15,"value":976},"Keeps useful mid-range information",{"type":9,"tag":18,"props":978,"children":979},{},[980],{"type":15,"value":981},"These filters help:",{"type":9,"tag":173,"props":983,"children":984},{},[985],{"type":9,"tag":18,"props":986,"children":987},{},[988],{"type":15,"value":989},"Reduce noise and make particles easier to see.",{"type":9,"tag":46,"props":991,"children":992},{},[],{"type":9,"tag":10,"props":994,"children":996},{"id":995},"_8-the-famous-duck-example-3d-reconstruction-concept",[997],{"type":15,"value":998},"🦆 8. The Famous “Duck” Example — 3D Reconstruction Concept",{"type":9,"tag":18,"props":1000,"children":1001},{},[1002],{"type":15,"value":1003},"Beautiful conceptual explanation.",{"type":9,"tag":18,"props":1005,"children":1006},{},[1007],{"type":15,"value":1008},"Idea:",{"type":9,"tag":61,"props":1010,"children":1011},{},[1012,1022,1032],{"type":9,"tag":65,"props":1013,"children":1014},{},[1015,1017],{"type":15,"value":1016},"A 3D object produces many ",{"type":9,"tag":24,"props":1018,"children":1019},{},[1020],{"type":15,"value":1021},"2D projections",{"type":9,"tag":65,"props":1023,"children":1024},{},[1025,1027],{"type":15,"value":1026},"Each projection has its own ",{"type":9,"tag":24,"props":1028,"children":1029},{},[1030],{"type":15,"value":1031},"2D Fourier transform",{"type":9,"tag":65,"props":1033,"children":1034},{},[1035,1037],{"type":15,"value":1036},"These are slices through a ",{"type":9,"tag":24,"props":1038,"children":1039},{},[1040],{"type":15,"value":1041},"3D Fourier transform",{"type":9,"tag":18,"props":1043,"children":1044},{},[1045],{"type":15,"value":1046},"If we collect enough projections:",{"type":9,"tag":18,"props":1048,"children":1049},{},[1050,1052],{"type":15,"value":1051},"➡ We can reconstruct the full ",{"type":9,"tag":24,"props":1053,"children":1054},{},[1055],{"type":15,"value":1056},"3D Fourier space",{"type":9,"tag":18,"props":1058,"children":1059},{},[1060],{"type":15,"value":1061},"Then:",{"type":9,"tag":18,"props":1063,"children":1064},{},[1065],{"type":15,"value":1066},"➡ Fourier inversion → real space 3D structure.",{"type":9,"tag":18,"props":1068,"children":1069},{},[1070,1072],{"type":15,"value":1071},"This is the ",{"type":9,"tag":24,"props":1073,"children":1074},{},[1075],{"type":15,"value":1076},"core mathematical principle of single-particle cryo-EM reconstruction.",{"type":9,"tag":46,"props":1078,"children":1079},{},[],{"type":9,"tag":10,"props":1081,"children":1083},{"id":1082},"_9-why-not-all-electron-microscopes-can-do-cryo-em",[1084],{"type":15,"value":1085},"🧊 9. Why Not All Electron Microscopes Can Do Cryo-EM",{"type":9,"tag":18,"props":1087,"children":1088},{},[1089],{"type":15,"value":1090},"Important practical insight.",{"type":9,"tag":18,"props":1092,"children":1093},{},[1094],{"type":15,"value":1095},"Cryo-EM requires special features:",{"type":9,"tag":61,"props":1097,"children":1098},{},[1099,1104,1109,1114],{"type":9,"tag":65,"props":1100,"children":1101},{},[1102],{"type":15,"value":1103},"❄️ Cryo holder (liquid nitrogen temperature)",{"type":9,"tag":65,"props":1105,"children":1106},{},[1107],{"type":15,"value":1108},"🎯 High-contrast biological objective lens",{"type":9,"tag":65,"props":1110,"children":1111},{},[1112],{"type":15,"value":1113},"⚡ Low-dose imaging system",{"type":9,"tag":65,"props":1115,"children":1116},{},[1117],{"type":15,"value":1118},"📸 Direct electron detectors",{"type":9,"tag":18,"props":1120,"children":1121},{},[1122],{"type":15,"value":1123},"Material science TEMs usually lack these.",{"type":9,"tag":18,"props":1125,"children":1126},{},[1127],{"type":15,"value":1128},"So:",{"type":9,"tag":173,"props":1130,"children":1131},{},[1132],{"type":9,"tag":18,"props":1133,"children":1134},{},[1135],{"type":15,"value":1136},"You cannot just use any TEM for biological cryo-EM work.",{"type":9,"tag":46,"props":1138,"children":1139},{},[],{"type":9,"tag":10,"props":1141,"children":1143},{"id":1142},"final-big-picture",[1144],{"type":15,"value":1145},"🧩 Final Big Picture",{"type":9,"tag":18,"props":1147,"children":1148},{},[1149,1151,1156],{"type":15,"value":1150},"This lecture teaches the ",{"type":9,"tag":24,"props":1152,"children":1153},{},[1154],{"type":15,"value":1155},"physics + math foundation of cryo-EM image processing",{"type":15,"value":192},{"type":9,"tag":1158,"props":1159,"children":1161},"h3",{"id":1160},"core-ideas-to-remember",[1162],{"type":15,"value":1163},"Core ideas to remember:",{"type":9,"tag":18,"props":1165,"children":1166},{},[1167],{"type":15,"value":1168},"⭐ Image contrast = amplitude + phase\n⭐ Cryo-EM contrast is mainly phase contrast\n⭐ Elastic scattering builds signal\n⭐ Inelastic scattering builds noise + damage\n⭐ Fourier space separates structural information by resolution\n⭐ Filtering improves visibility\n⭐ 3D reconstruction uses many 2D projections in Fourier space",1775084311000]