EDT/Collect for DigitalMicrograph

Transcription

1 May 2016 (Provisiona) EDT/Coect for DigitaMicrograph Data Coection for Eectron Diffraction Tomography EDT/Coect Manua 1.0 HREM Research Inc.

2 Introduction The EDT/Coect software has been deveoped by HREM Research Inc. in coaboration with the AnaiteX company ( The EDT/Coect Digita Micrograph pugin aows the user to Coect beam-tit Eectron Diffraction Tomography 3D data sets. Genera enquiries on the EDT/Coect for DigitaMicropraph shoud be sent to: HREM Research Inc Matsukazedai Higashimatsuyama Saitama Japan emai: website: Enquiries on EDT/Coect of a technica nature shoud be directed to: AnaiteX company emai: support@anaitex.com website: The proper reference to the data coection method as of January 2013 is M. Gemmi and P. Oeynikov. Scanning reciproca space for soving unknown structures: energy fitered diffraction tomography and rotation diffraction tomography methods. Zeitschrift für Kristaographie - Crystaine Materias: Vo. 228, No. 1, pp Copyright Statements Copyright 2016 HREM Research Inc. and AnaiteX A rights reserved. This manua is protected by internationa copyright aws and treaties. Unauthorized reproduction and distribution of this manua, or any portion of it, wi be prosecuted to the maximum extent possibe and may resut in severe civi and crimina penaties. Portions of this document were prepared by HREM Research Inc. by editing the materias suppied by AnaiteX. DigitaMicrograph is a trademark of Gatan Inc. 2

3 Instaing the program EDT/Coect is avaiabe as a pugin to DigitaMicrograph of the Gatan microscopy Suite (GMS). As of 2016 the foowing GMS versions are supported: 32 bit: GMS 1.x and GMS 2.x ; 64 bit: GMS 2.x and GMS 3.x; EDT/Coect is avaiabe in the 32 bits version. The EDT/Coect software contains ony proprietary ibraries such as, for exampe, Inte MKL. Software requirements The foowing is a ist of the software requirements necessary to run the EDT/Coect pug-in: - DigitaMicrograph (GATAN TM ) - USB Key Driver - HREM Mouse Too Pug-in (Free-ware downoadabe from - IPU Pug-in (Free-ware downoadabe from - Gatan EMContro Pug-in (a pug-in supported by Gatan to communicate with a microscope) - AnaiteX TEM Server (pease consut the manua for the TEM server) Software Instaation Instaing USB Key Driver The user key driver shoud be instaed by foowing the instructions given by the key driver instaer. The key driver instaer comes with EDT/Coect, or you can find it on our web site. Instaing EDT/Coect Pug-in The pug-in can be instaed by drag-and-drop copy to the foder PugIns (The PugIns foder shoud exist under a norma instaation of the DigitaMicrograph.) When the DigitaMicrograph is aunched after pacing the pug-ins into the PugIns foder, EDT/Coect menu commands wi appear under EDT/Coect menu. Instaing Mouse Toos A the fies reating Mouse too pug-in can be instaed by drag-and-drop copy to the foder PugIns. (The PugIns foder shoud exist under a norma instaation of the DigitaMicrograph.) When the DigitaMicrograph is aunched after pacing the pug-ins into the PugIns foder, the Mouse too wi appear as an addition to the standard toos. Instaing IPU Pug-in EDT/Coect uses some functions based on the Inte MKL (Math Kerne Library) provided by the IPU pug-in. A the fies reating the IPU pug-in can be instaed by drag-and-drop copy. Pease consut the ReadMe fie that comes with the IPU pug-in. Instaing AnaiteX TEM Server Pease consut the manua for the TEM server. If you need any hep to insta/use the TEM Server, pease contact with AnaiteX directy. 3

4 Accessing the pugin from the DM menu Each modue is accessibe through the main DM menu EDT/Coect and has a unique name that represents the content of the corresponding modue. The avaiabe commands through the main menu are: Caibration the TEM cois caibration; Coect Data the main data coection modue; Settings changing the program settings (for service operators, not recommended to use); Hep getting hep on the pugin. About dispays the About diaog with the pugin information. 4

5 Pugin settings After the instaation of the EDT/Coect pugin in the DigitaMicrograph the user shoud set up some parameters so that the pugin knows what CCD cameras can be used, the diffraction pattern scae bars (pixe size) for accessibe camera engths, avaiabe sampe hoders and etc. In order to access the pugin settings pease choose the Settings menu item from the EDT/Coect DM main menu. The foowing diaog wi show up: CCD settings The pugin wi automaticay identify a cameras avaiabe to DigitaMicrograph that can be accessed through the Current camera drop down ist. For each camera the user can set the Oversaturation Leve (wi be used by the EDT-Process software package to count oversaturated pixes). IMPORTANT: The user must add caibration vaues (pixe size) at east for a singe TEM camera ength vaue that is panned to use. These vaues wi be used by the EDT-Process program in order to cacuate correct d-spacing vaues of the recorded diffraction patterns. For diffraction mode caibration: 1. Seect SA DIFF from the Caibrations: Mode: drop down ist (defaut is SAMAG); 2. Press Add button in order to add a caibration item to the ist. (If you need to remove the seected caibration item, then seect the ID to be deeted, and press the Remove button.) The foowing diaog, that shows defaut (uninitiaized) vaues, wi appear: 5

6 3. Fi in the vaues: (A) ID the integer identifier (unique index) of the magnification/camera ength; (B) Mag/C.L. the magnification vaue or camera ength (in [mm]) that is currenty set at the TEM; (C) Scae the pixe size. If you don t know the correct scae vaue, escape the diaog by pressing Cance button. You can obtain the correct scae vaue as expained beow. Input exampe 4. Press OK. 5. Repeat the steps 2-4 for a camera ength that are used for the data coection in diffraction mode. How to get a correct scae vaue In order to get the correct scae vaue (angstrom/pix) the user can use the scae bar accessibe from the recorded eectron diffraction pattern using standard DM acquisition. 1. Set the desired camera ength on your TEM. NOTE: on some microscopes the camera ength changes depending if the fuorescent (view) screen in the coumn is up or down (FEI TEMs). If this is the case pease put the screen up so that your CCD can record a rea diffraction pattern. 2. Acquire a diffraction pattern at binning 1 (important!) and any exposure (can be very short as the diffraction data itsef is not needed). 3. After the pattern acquisition is done right-cick on the pattern with the mouse and seect ImageDispay... from the context menu: 6

7 4. Find and seect the item Image à Caibration on the eft: 5. Find the Scae vaue in the right part of the Image Dispay Info diaog under Dimensions group. NOTE: DM has two scae vaues for x- and y-coordinates of the image (for exampe, if image binning aong x-axis is different from the binning aong y-axis during the acquisition. Currenty EDT/Coect supports ony a singe scae factor. NOTE: DM uses reciproca nm units (nm 1 ) for the scae factor. EDT/Coect uses reciproca Ångström units (Å 1 ). For the above scae vaue taken from DM ( [1/nm]) use the vaue of [1/Å] when adding a caibration item to the ist in the EDT/Coect CCD settings diaog. 7

8 Sampe hoder settings This tab wi hep you to maintain the ist of sampe hoders that can be used on your TEM. The user can add/remove (using Add and Remove buttons respectivey) sampe hoders from the ist: The Remove button wi remove currenty seected sampe hoder from the ist. When pressing the Add button the foowing diaog wi appear: Here the user can specify: the name of the hoder (Name edit box); the titing imit of the hoder in degrees (apha tit, Limit edit box); the initia deay (in miiseconds) of the stage before it wi start titing (First Stage Deay). This vaue is needed if order to have some deay before the CCD wi be activated in the View mode so that the user can see there is the crysta wi move once the stage wi start titing. The consequent stage deay vaue is reserved for the future use. 8

9 Pug-in parameters The Parameters tab is used to set up the EDT/Coect internas. The TEM Mode caibration group can be ony set after the first data coection has been processed by the EDT-PROCESS software. EDT-PROCESS wi report the Apha Tit Axis and the need of the inversion of the beam tit direction and/or the Ewad sphere. The Coect Data group shoud be used ony for the cameras with a phosphor screen (such as Gatan Erangshen ES500W) in order to introduce some deay between the consequent acquisition of diffraction frames getting rid of the previous decaying diffraction pattern that might have strong intensities that coud affect the current frame. In a other cases it is safe to remove both check-box marks. 9

10 TEM cois caibration Since on some eectron microscopes (for exampe JEOL) the changes of cois and enses are done in interna units the caibration of these cois is needed in order to: Convert the arbitrary units into physica units (e.g. nm or degrees); Compensate the beam shift induces by one ens using the other. The caibration of each coi is done in 2 dimensions: aong X- and Y- axes of the corresponding coi. The caibration is performed automaticay by the program after pressing the corresponding Caibrate button. The caibration must be performed in the DIFFRACTION mode of the microscope. For the TEM mode of the JEOL microscope insert the SAED aperture and focus the beam into the point. For the NBD mode seect the size and the brightness of the beam (same as wi be used ater for the data coection) and focus the beam into the point. Pease seect the Caibration from the EDT/Coect menu in order to caibrate current TEM cois. The foowing diaog wi be shown: Beam tit Projector coi For the 3D EDT data coection pease use the foowing steps: 1. Seect an empty area on your grid; 2. Insert a smaest SAED aperture accessibe on your microscope; 3. Spread the beam; 4. Switch into diffraction mode on your TEM; 5. Set the desired camera ength; 6. Center and focus the centra spot; 7. Check the Recacuate ange on the Caibration diaog; 8. Set some vaue in Change vaue: edit box for the Beam tit cois. An initia vaue for JEOL TEM can be 1000 units for the start; 10

11 9. Press Caibrate button and wait whie the caibration is finished; 10. Repeat steps 8 9 for the Projector coi. CAUTION! Be carefu with the direct exposure of the CCD to the eectron beam! Use minimum intensity beam (spread the beam using the Brightness knob of the JEOL TEM; use high spot size, for exampe 5; insert sma SAED aperture in TEM mode). The caibration of the seected coi is done automaticay according to the foowing steps, when you press Caibrate button. The caibration program 1. reads the user-suppied Change vaue from the pane (et s ca it CV vaue); 2. reads current coi vaues for x- and y-axes (et s ca them as X 0 and Y 0 vaues); 3. records the diffraction pattern (origina pattern); 4. changes the x-axis vaue of the coi by the CV vaue (so it becomes X 0 +CV); 5. records the diffraction pattern (X-modified pattern); 6. changes the x-axis back to the origina X 0 vaue and changes y-axis vaue of the coi by the CV vaue (so it becomes Y 0 +CV); 7. records the diffraction pattern (Y-modified pattern); 8. restores the coi y-axis vaue back to Y 0 ; 9. cacuates the shifts of the spot using normaized cross-correation; 10. if the shifts is sma and the check box for Automatic Change vaue is seected, the CV vaue is automaticay doubed and go to the step 4; 11. saves the caibration matrix (the direction of the coi x- and y-axes and the measured deviations aong x- and y-axes). The correct coi caibration images shoud ook simiar to the foowing: Current Shifted Cross-correation The Current pattern is a sum of 3 recorded diffraction patterns the origina and 2 with induced changes aong x- and y-axes of the coi. The 3 spots seen on the Current pattern can be interpreted as shown on the Figure beow: 11

12 Y The spot after y-axis change X The spot after x-axis change The origina spot NOTE: the caibration wi be more precise if the 2 spots obtained from the induced changes of x- and y-axes of the coi are wi separated (cose to the edge of the CCD frame). These positions depend on the Change vaue for the corresponding ens. The Shifted pattern shows the ast pattern with the deviation of the y-axis of the coi. The Cross-correation pattern is the sum of 2 individua cross-correation patterns: (1) the origina pattern and the pattern where the x-axis has been changed; (2) the origina pattern and the pattern where the y-axis has been changed. Since in each case the cross-correation shows a singe peak then the sum of the 2 cross-correation functions must show 2 we-separated peaks. 12

13 Coecting 3D EDT data sets NOTE: It is strongy recommended to run the TEM cois Caibration modue prior the data coection. The data coection of 3D Eectron Diffraction Tomography data can be performed using the Coect Data modue from the main EDT/Coect menu. The Data Coection diaog box wi be shown as it can be seen on the foowing figure: The group box Sampe Hoder can be used to seect the appropriate sampe hoder that is currenty in use (see section Sampe hoder settings on how to manage a ist of sampe hoders). It is required to choose the sampe hoder prior the data coection. The actua imit of the apha-tit anges wi be shown beow the seected sampe hoder type ( Limit (deg): 70 on the figure above). The group box Coect Data shoud be used for the data coection. The settings that wi be used for the data coection are: Coection type can be chosen from the Coect drop-down box (currenty Rotation 3D (manua) ); The foder where the acquired frames wi be stored can be chosen using the browse button ( Foder ). The seected foder wi be show next to the button, for exampe, ( C:\Users\VALUEDGATANCUSTOMER\Desktop\Test\ on the figure); The Beam tit range (in degrees) corresponds to the fu ange that wi be covered by the beam tit of TEM. In case of 3 the beam tit wi vary from 1.5 to In this exampe the beam tit wi cover the anges from 0.5 to +0.5 (1 in tota); 13

14 The Beam tit step (in degrees) specifies the beam tit step that wi be used in order to cover the range of the beam tit anges specified in Beam tit range. In this exampe the program wi change the beam tit in the range from 0.5 to +0.5 (covering 1 ) with a step of 0.5. This means that the beam tit wi be consequenty set to the vaues of 0.5, 0 and +0.5 (3 frames). If we set the Beam tit range to 3 and keep the step of 0.5 then the beam tit wi be consequenty set to the vaues of 1.5, 1, 0.5, 0, +0.5, +1 and +1.5 (7 frames); The Series overap (in degrees) defines the overap between consequent goniometer tits. This vaue is in order to compensate the mechanica imperfections of the stage. In idea case the goniometer shoud tit by the same vaue as the Beam tit range (1 in this case). However, if the vaue of Series overap is different from 0 then the rea goniometer apha-tit wi be Beam tit range minus Series overap (1 0.1 = 0.9 in our exampe). The Series overap vaue can be kept as 0.2 for most data coections; The Start deay (miiseconds) and the Beam bank check box are used for some types of CCDs that are sensitive for the beam position changes. Some CCD cameras (such as Gatan ES500W) use a fuorescent screen so that there can be a trace eft by the strong beam whie it moves during the beam tit or shift. It may decay sowy and can be noticed on the CCD. In order to compensate for these effects pease check the Beam bank and put some deay ( ms shoud be generay enough). NOTE: The coected data set must occupy an individua foder. Every new data coection must be pointed into a new foder otherwise a previous data wi be overwritten with the new dataset! 14

15 Data coection step-by-step In order to start the data coection the used needs to press the Start button at the bottom of the pane. The data coection contains the foowing steps: 1. Check the sampe height (using the Test Focus or Test Wobbe buttons); 2. Coect the beam tit data (using the Coect Data button); 3. Tit the stage (using the Tit stage button); 4. Manuay track the crysta using the CCD camera; 5. Repeat from the step 1; 6. Finish the data coection by pressing the Cance (Finish) button. Checking the sampe height There are two ways to check the crysta height (in imaging mode!): (i) the dynamic wobbe of the beam by titing and (ii) subtract two frames recorder with opposite beam tits. The dynamic wobbe test is simiar to the JEOL X-WOBBLE button. In this case the data coection program induces 2 opposite beam tits (+/ 0.5 in our case) and switches the CCD into the view mode for the observations. The correct sampe height wi be the one when the crysta reative movement wi be minima. The frame subtraction produces the foowing images in the case of (eft) the correct sampe height notice the average gray eve of the inner part of the SAED aperture with minimum number of distinguishabe features and (right) the sampe height is wrong there are 2 shadows of the crysta corner. Two shadows of the crysta due to the sampe movement caused by the beam tit 15

16 Coecting the data The beam tit data wi be coected automaticay by the program. A the frames wi be saved to disk in the DM3/DM4 format. The typica status of the data coection is shown on the figure beow: NOTE: During the data coection of the beam tit series a buttons (except Cance) wi be disabed. Titing the stage As it was mentioned previousy, the stage wi be tited by the ange that is cacuated as the Beam tit ange minus the Series overap ange. In the case that is presented in this manua the stage tit wi be equivaent to 0.9 (1 0.1 = 0.9 ). The data coection program wi switch the CCD into the view mode for the crysta tracking. Manuay tracking the crysta This is the most crucia step during the data coection. The user must move the crysta back so it wi occupy the appropriate position so that the next beam tit series can be coected. The crysta tracking can be easiy achieved with the X-Y stage contro of the microscope after the stage has been tited. 16

17 Data processing A the recorded frames and the data coection og fie wi be stored in the seected foder for the current data coection. Do not change/erase/modify the fies in the foder! The whoe foder however can be moved to any other ocation. The coected data set can be further processed with the data processing program EDT-PROCESS from AnaiteX. Bug reporting There are og fies created by the program during every run. These ogs are stored in a specia foder that depends on the Windows version. 17