Gatan K2 Summit, User Manual

Page 1: ...aseTM Direct Detection Camera User s Guide Model Number 1000 1000 S 1000 B and 1000 U Document Part Number 1000 40004 Revision 01 Gatan Inc 5794 W Las Positas Blvd Pleasanton A 94588 Tel 1 925 463 020...

Page 2: ...Started with the K2 Direct Detection System 14 Power on Sequence for K2 Base 14 Power off Sequence for K2 Base 15 Power on Sequence for K2 Summit 15 Power off Sequence for K2 Summit 17 Setting Tempera...

Page 3: ...on 35 Shutter Connections and Signal Configuration 36 Base Camera Linear Mode Operation 36 Switching Between Base and Summit Modes 37 Care of Detector 38 Temperature 38 Anneal Cycle 38 Auto Retraction...

Page 4: ...uper Resolution mode 20 figure 1 14 Option to skip gain reference collection 21 figure 1 15 Suggested gain reference exposure factor 21 figure 1 16 Settings for K2 Summit linear mode gain reference 22...

Page 5: ...mode settings 35 figure 1 40 Shutter settings tab 36 figure 1 41 Auto Retraction Delay setting 39 figure 1 42 Gatan logo and Camera Inserted setting 39 figure 1 43 Typical DM setup DigitalMicrograph...

Page 6: ...ething may have the potential to cause damage to the equipment or fail to operate correctly if the instructions are not followed Disclaimer Gatan Inc makes no express or implied representations or war...

Page 7: ...must appear on all shipping documents to ensure that proper actions will be taken to repair or replace the instrument Support Gatan Inc provides free technical support via phone fax and electronic mai...

Page 8: ...m 3838 x 3710 to 7676 x 7420 Again the processing is all done on full frames in real time as the images are collected In addition the camera employs a pixel design giving radiation hardness 10x greate...

Page 9: ...lec ead noise of th tection is the ain variations ncy DQE of and by large v his is also true ir ultimate pe K2 Summit re he benefit of sited by electr e Quantum Ef ion Camera U of low dose d ase radia...

Page 10: ...em Micrograph ode that we ca K2 Base and n camera syst Summit uniqu the individual dout with the e Counted and on and O on mode take physical pixe ger than the 5 al in a small c ion Camera U ions es i...

Page 11: ...sor K2 was specifically designed to count at a typical Cryo EM dose rate of 10 20 e pixel s allowing a 20 e 2 low dose image to be recorded in 1 2 s at a magnification equivalent to 1 pixel To do so t...

Page 12: ...an inates with su er of pixels in olution mode t t defined by th y designed suc lectron deposi electronics is the center of ng of the effe even higher the field of vie apture much m ion Camera U on pr...

Page 13: ...ensor to the electron beam when the camera is not in use Based on the results to date the lifetime of the K2 detector is estimated at 5 billion e pixel Considering exposure rates of 100 electrons pixe...

Page 14: ...t is open or power on the PC if it is off 2 Turn on the K2 digitizer blue K2 box near the camera and TEM figure 1 4 K2 digitizer 3 Wait at least 3 minutes after powering on the K2 digitizer 4 Launch D...

Page 15: ...etely wer down the he settings bu em OFF butto gitizer blue b C if desired for K2 S power off is open or po to the Therm wer switch on Controller to 2 digitizer blu Direct Detecti Base ou can leave th...

Page 16: ...igita and K2 Base igitizer minutes after Micrograph g button ham em ON 2 b alMicrograph Direct Detecti powering on DM mmer wrench button Wait fo h interface d ion Camera U n the K2 digiti 1 in the K f...

Page 17: ...pletely power down the K2 camera 1 In DM Click the settings button hammer wrench in the K2 Direct Detection palette 2 Click the System OFF button Wait about 10 seconds or open the logs and watch for t...

Page 18: ...0 K2 Sensor temperature Anneal Cycle Regular annealing heating to 50 C of the sensor helps maintain top performance of the sensor by reducing background levels and levels of surface contamination Anne...

Page 19: ...mmit K2 Base operates in charge integration mode When the Summit camera version is selected the three modes available from the K2 Direct Detection palette are Linear Counted and Super Resolution Linea...

Page 20: ...the electron positions resulting in a higher resolution image with the best performance possible Raw images are dark subtracted gain normalized and processed in hardware to detect individual electrons...

Page 21: ...n skip parts of this procedure if you already have a good reference and don t want to update it or if you wish to leave the procedure part way through and come back later For instance at this step you...

Page 22: ...reference If you click the Expert Mode box you have the option to restore default values or select and save your own values for linear mode gain reference collection if you want a higher quality gain...

Page 23: ...osure factor which could result in low image quality you see the warning message pop up again and have to reconfirm your choice You are now asked to adjust the beam to the selected dose rate Because s...

Page 24: ...ssary images and calculates any needed corrections When the success message appears click OK figure 1 22 Linear mode gain reference success message K2 Summit Counted and K2 Summit Super Resolution Nex...

Page 25: ...eference option Next the linear gain reference is automatically uploaded These references are used for correcting the images in the processors before electron detection and counting The Exposure Setup...

Page 26: ...he previous s and K2 Base ngs for K2 S ert Mode sett default values tep You may Direct Detecti ummit linear tings s the beam ne y need to chan ion Camera U r mode gain eeds to be dim nge spot size Use...

Page 27: ...t h the collectio ngs for inten Super Resolu When it is d ar mode gain Direct Detecti t reminder r Resolution m am very close ecommendat t parameters a on nsity and num ution dose rate done the refer...

Page 28: ...nce This means that regular dark reference update can save the work of updating the gain reference which typically takes longer due to the large exposure factor recommended for minimizing DQE derating...

Page 29: ...all exposure lengths This is why we look at dose rate The camera is always operating at a fixed 0 0025 second exposure 400 frames per second in Summit mode The DM exposure length determines how many o...

Page 30: ...tinuous low resolution image with the entire sensor field of view This is to allow the user to quickly conduct a sample search using the camera Focus mode displays a continuous image at higher resolut...

Page 31: ...pixel dose rate e pix s when e on camera s been done o l dose is disp e and total do V basis That e calibration i to only start i sired level or k the beam le 2 Setup wind ollecting data acquisition m...

Page 32: ...added to all of them Shutter Delay pre dose delay mode specific settling time View Acquire Dose Fractionation figure 1 36 Advanced View Options settling delay option Defect Correction Defect pixel ma...

Page 33: ...ignment and stigmation with live diffractograms Dose Fractionation Dose Fractionation mode provides straight to disk capture at 40 fps 0 025s per frame in Summit mode and approximately 10 fps in Base...

Page 34: ...actionation he right of the rrection Direct Detecti dose fractio ght and with is selected fo y the exposur n the Dose Fr ay time if a di amera etting n mode open e K2 Dose Fra ion Camera U onated data...

Page 35: ...orrelation Filter drop down item optimizes the automatic alignment and frame accumulation using a customized image filter It is important to note within the context of discussing dose fractionated ali...

Page 36: ...sensor T fficient pre ex Signal Co go to K2 Setu tab ration rs the same ra ng in the linea the camera to e significant b r high perform exposure tim dations for K2 en and net sy for typical si es exce...

Page 37: ...y the read noise equivalent dose which for the Base Linear mode is approximately 0 1 primary electron equivalents per pixel per second at 300kV the Summit camera s corresponding value in linear mode i...

Page 38: ...lines are not obstructed and adjust the pressure regulator to bring the flow back to the original level If the water flow stops while the Peltier cooler is on damage to the camera may result WARNING...

Page 39: ...on time to 60 Retraction D n the camera l he Camera Vi n logo and C tection ly while the c italMicrograp Direct Detecti etract if you a to a safety fe 00 seconds Delay setting ights up when iew palle...

Page 40: ...g Do not attempt to clean the CMOS sensor yourself as damage can result If the surface of the CMOS sensor becomes dirty or scratched contact Gatan for service Sensor replacement Recommended to only be...

Page 41: ...sure he communica ad automatica Direct Detecti a within D 7 minutes to b essary time to y with the SSD y for K2 Ca of how DM sh es go to Win e to display T p DigitalMicro libration cation on TEM ated...

Page 42: ...during magnification calibration 1 Choose Microscope Calibrate image 2 Follow the instructions on screen figure 1 45 Magnification calibration instructions A red line appears on the image 3 Position...

Page 43: ...Calibration confirmation 7 Click Yes to complete the calibration The calibration can be checked on the calibration table containing pairs of value the nominal microscope magnification and the calibra...

Page 44: ...shows the table of magnification calibrations stored for the current imaging device High Magnification Record a lattice image of the crystalline sample figure 1 49 High resolution image of sample to...

Page 45: ...bration instru ation instruct agnification c Direct Detecti n peaks in th am follow the ffractogram in e red line on t procal unit an uctions tions and click alibration in t ion Camera U he calculate...

Page 46: ...e xels to film d mputer 00 kV 0 0 and K2 Base bration settin K2 3838 50 8 f 8 f 0 30 peak 0 25 at 0 5 of p Ga Direct Detecti ngs 2 Base 1 8 x 3710 full fps full fps full fps physical Nyqui atan Micros...

Page 47: ...ange of additional applications to make electron microscopy easier and more efficient The K2 camera is retractable and is mounted below the TEM in a standard Gatan camera housing and allowing simultan...

Page 48: ...xposure length because the derating metric scales with exposure time due to the fact that while random noise sources accumulate as the square root of exposure time fixed pattern noise accumulates line...

Page 49: ...modulus realfft imga top left bottom right imgb top left bottom right 2 number ratsize 128 image rednpssum realimage 4 ratsize ratsize image rednpsdiff realimage 4 ratsize ratsize getsize npssum widt...