Setting up the SEM

the following conditions should be considered before setting up sem amics measurements § after changing a sample, it is necessary to give the system time to stabilize (vacuum, beam current) to reduce bse drift the time needed depends on the specific hardware platform, at least 20 minutes is recommended § when setting up the sem for amics measurements the aim is to optimize x ray counts therefore, a larger aperture (if applicable) and a larger spot size are recommended § amics is flexible and allows different beam energies (kv) that be used for measurement however, keep in mind that due to the influence of beam energy on peak geometry, if the sample is measured at 15 kv the ore type list should also be collected/created from 15 kv spectra § the eds spectrometer should be calibrated regularly energy channel shift can impact the accuracy of mineral identification in amics § set up the contrast and brightness on the sem so that the bse range is between 0 255 · the background/epoxy should have a bse level < 15 · gold (au) or the brightest phase in the sample should be just below 255 step 1 set up the sem the specific workflow to set up each sem platform will vary depending on the exact model and also software version installed on the sem as such the following instructions will provide a workflow as a best practice, using examples from various hitachi sem platforms to exemplify each step beam calibration and system setup beam calibration is generally something required for tungsten based instruments, and is required to ensure consistent spectral results between analytical batches users should verify that the system is running in high vacuum mode, as some sem do have the option to run at partial or variable pressure modes users should then verify the correct accelerating voltage and working distance have been set for the instrument these are important to ensure relevant elemental lines are visible and to maximize detector input counts, respectively energy calibration to ensure amics correctly classifies materials it is important to ensure the eds detector system is working properly, and in the case of multi detector system that the energy spectrum of the detectors are all aligned to do this the sample stage needs to be moved to the included standard hole location, which should contain both a copper and quartz standard in the below example, the reference standard is noted by the small dark circle users can move to the reference standard by right clicking the mouse over the circle and selecting "move hw to position" if running amics investigator on a m4 or m4plus tornado the same procedure can be completed to find the energy calibration standard otherwise if using the native espirt application to collect the bcf data for later processing via amics process, users should follow the calibration instructions per the m4 or m4plus tornado user manual the copper standard should then be located, which will generally be the brighter of the two reference materials if the provided standard is being used depending on the sem system being used, either set the beam control to "spot" mode or adjust the position and magnification of the sem image to ensure the copper standard occupies the whole screen then open the bruker espirt application, log in per normal procedures and then click on the "system" button to access the calibration menu this will change the main display and also change the menu tabs above the main display, giving the option to select "spectrometer" the main display will now change to the x ray energy calibration window on this interface ensure the calibration element has been set to copper k alpha depending on the installation confirmation and system usage, check the correct "pulse throughput" and "energy range" required in general for amics, the standard "pulse throughput" will be the highest cps rate available (i e 600,000 or 1,000,000 cps for full size systems and 275,000 cps for compact systems) and the "energy range" should be set to 20 kev finally, clicking on the "down" arrow next to the start button will bring up a "precision" pop up window, where the "precise" setting should be selected the "start" button can then be pressed to start the automated calibration process upon completion of the calibration process, users should ok the new calibration parameters and take note of the new "fwhm at 0 0 kev" and "fwhm at 8 0478 kev" values, and ensure they do not exceed the prescribed value image calibration for the use of data acquisition on amics investigator on sem platforms, the brightness and contrast of the acquisition image also need to be calibrated to ensure consistent measurements between batches of specimens the following workflow for sem calibration is based on the use of the quartz calibration standard provided during the instrument installation users should adjust the workflow if another brightness and contrast standard setting is being used step 2 set up the specimen the quartz standard should be first located and the sem viewing area should be set such that the quartz standrard occupies half the screen and per image above the histogram bse calibration application can then be used to adjust the brightness and contrast settings within the sem control panel to match workflow requirements the workflow for this process is shown in the image below, with the first step to run the amics bse historgram calibration app once the application fully run, a blank/black command line window open, which need to be minimised, the application will then pop up a windows to request a lower bse calibration level, which for standard amics anlaysis should be set to 15 you will then be prompted for the upper bse calibration level, which for standard amics analysis should be 110 the lower threshold for standard amics analysis is the resin, to ensure correct background segmentation however, users can either use a different lower bse threshold standard or adjust the value of the lower bse depending on their workflow requirements the higher threshold for standard amics anaysis is quartz however, any material can be used for a higher threshold depending on the workflow requirements as per the pop up warning, once the ok button is pressed, the user should click and drag an area on the screen which cover both the quartz standard and the mounting resin, as per the example image below once the mouse is released a new window containing the histogram calculated for the selected area will appear this histogram will also contain two blue lines with labels 15 and 110 (or whatever the user specific value) using either the hard panel or the onscreen controls change the brightness and contrast of the image so that the left hand peak sit over the left hand line, and the right hand peak sits over the right hand line once this is achieved, the software can be closed by clicking the "x" in the top right hand corner the amics bse histogram can be download here https //github com/bruker amics/bugs features/releases/download/amics histogram/amics histogram v0 1 exe and a pdf user manual for this applciation can be found here https //github com/bruker amics/bugs features/releases/download/amics histogram/amics histogram app v0 1 pdf beam calibration during normal operation of the sem the speed of the bse image scanning can be adjusted, which allows users to compromise between acquisition time versus image quality however, during automated amics analysis, the change in image quality at a faster scan speed can affect the accuracy of the beam placement during matrix and segmentation mapping mode to try to correct for some of this in accuracy amics has a beam calibration function accessible from tools and investigator the beam calibration option in tools can be found in the main menu while in investigator it can be found in the others menu option in both cases, the same beam calibration menu will be accessed, and the workflow to calibrate/correct the beam positioning will be the same note the beam calibration workflow in amics is not the same as that in the sem, and is only designed to adjust for the difference in beam positioning and does not affect the beam alignment or spot size, which can only be changed from the sem software to perform a beam position calibration select the desired scan speed to be calibrated using the drop down menu next to the " scan speed " item note amics will always use the slowest/longest scan speed as the reference speed move the sem position to include and area of the sample or standard containing a clean clear image, preferably with sharp edges and particles located evenly distributed throughout the field of view focus the image to ensure as sharp edges as possible on all visible particles in the field of view select the " calibrate " option, and click " yes " to confirm an appropriate image is in view on the sem amics will then acquire two images, one at the desired scan speed for calibration and the second at the reference speed the main view will then be populated by these superimposed images, which will be gridded up into a 10x10 grid (highlighted in red in the image above) clicking the " < calc " button will generate a set of offsets for each cell, shown on the left hand panel, to best align the reference image to the original image the quality of the calibration can then be tested by clicking the " apply " button the beam position offsets can then be saved for the specified scan speed by pressing the " save " option once this process is completed for a specified scan speed, amics will use these calibrated offsets to correct beam position during point placement note this calibration process can only assist in correcting for beam position difference due to image noise at a fast scan speed, but the quality of the calibration will still be lower ata faster scan speed as such it is highly recommended to not use speeds faster/lower than 8us