Target Mineral Quant

introduction one of the most powerful and unique features of amics is its ability to link x ray chemical analysis to a spatial location on any sample this unique ability to automate this process means that users now have the ability to better understand the elemental deportment of elements of a larger scale with statically meaningful data points the target mineral quant (tmq) function in amics leverages this ability of amics to add another powerful tool for elemental assessment, allowing users to now selectively perform corrected quantification at the particle or grain level, to provide a more detailed understanding of elemental deportment in a sample some of the key features of the tmq features are filtering and sorting grains and creating summed spectra per grain, which provides bulk spectra for a grain exporting grain tables containing coordinates and elemental composition with the ability to align with fiducial points, for realignment on 3rd party tools usage guide step by step instructions tmq can be accessed via the mineral quant tab above the main data visualization panel the tmq interface will update the main data visualization panel to contain an upper and lower section, with the upper frame containing grains that have passed the user filtering the and lower section showing all grains which failed the filtering the right hand property interface provides the options for selecting and filtering grains for the tmq feature to perform quantification, the user must have pre selected the eds quantification recipe from bruker espirt software the option to load or update the quantification method is available in the standards ribbon tab at the top of process on the standards menu ribbon, the quantification option will have an update method list, which will load all available recipes from espirt, and allow the user to select which recipe options to make available in amics once the appropriate recipe options have been selected, the exact recipe to use for quantification can then be selected by opening the method drop down menu note! to able to select quantification recipes or perform any post processing quantification requires bruker espirt software to be running in the background amics will not execute espirt automatically and will show an error if the user attempts to perform any quantification without espirt running first the tmq filter parameters allows users to sort and find target grains containing specific properties for quantification, using the following filters having mineral this filter will isolate grains containing one or more specified species from either the primary spectra list or group of spectra the selection option will change based on what list if being used in the current result standards list on the left hand side panel minimum area this filter will isolate grains with a total area greater than the set value, measured in square microns maximum area this filter will isolate grains with a total area less than the set value, measured in square microns minimum bse this filter will isolate grains with an average bse greater than the set value maximum bse this filter will isolate grains with an average bse less than the set value min radius (micron) this filter will isolate grains with a radius greater than the set value in microns the measured radius is the farthest distance from a calculated centroid filter by count this check box will enable or disable filtering the ability to isolate particles containing more grains of a specific target mineral mineral count this specifies the minimum number of target mineral grains that must be present in a particle, used by the filter by count option above once the appropriate filtering setting has been set by the users, the results of these settings can be tested and checked by clicking on the filter! button if the resultant number of the population of particles or grains which passed the filtering (as displayed in the upper portion of the main display) is not optimal, users can adjust the filtering parameters and refilter until an appropriate number and population of particles or grains are achieved after filtering, each particle or grain which passed the filter process, shown in the upper portion of the main data visualization panel, will display a blue crosshair that pinpoints a theoretical position for the summed spectra the cartesian coordinate for each of these crosshairs is listed in the quantification result panel at the base of the main data visualization panel, in the column headed center position the columns of the quantification result panel are center position list the cartesian coordinate of each of the theoretically calculated centroid locations based actual position of acquired x rays center reference list an alternative central coordinate to allow 3rd party software and equipment to realign the center position to a known fiducial point shape factor list of the calculated aspect ratio of the filtered particles or grains area (pixels) lists the number of pixels within each filtered particle or grain bse(max) the highest bse value measured for all pixels within each filter particle or grain xrays this lists the number of x rays uses to calculate the summed spectrum for each filtered particle or grain total count this lists the final total count of the calculated summed spectrum note! this crosshair is a calculated theoretical position of the created summed spectra, which is the sum of all the spectra collected across the surface of the particle or grain this theoretical position is based on minimizing the residual of this point to all the actual x ray points to quantify the filtered particles or grains, based on the calculated summed spectrum, can then be executed by clicking the quant now! button once the button is pressed, amics will quantify each of the summed spectra based on the selected eds calculation recipe the result of the quantification is then displayed in the quantification results panel, with additional columns added after the total count column or each of the elements all the data contained in the quantification results panel can then be exported either by copying the data and pasting it into any 3rd party software as text, or directly exported and saved as a text file to copy the data for pasting, click the copy button located on the top right hand side of the quantification result panel to export the data and save it as a text file, click the save button located next to the copy button this will bring up a file interface window to select where to save the final text file to allow the tmq workflow to be standardized there is an option to save the filtering parameters and also to restore these parameters this is achieved using the save search! and restore search! buttons located below the quant now ! button when the save search! button is pressed a user interface will pop up asking for a file name, which will be used as the file name used to identify the filter parameters clicking the restore search! button will bring up the amics tmq file manager window, which will allow users to manipulate which filtering parameters are available in the measurement the new interface will allow users to do the following rename allows users to change the file name used to reference and identify filtering parameters delete allow users to remove filtering parameters from the available list of parameters import allow users to copy over filtering parameters developed from other measurements export allow users to save a copy of the filtering parameters file to another location for use by another measurement note! the filter parameters are stored as a json text string, and there is currently no mechanism to check that the filter parameters imported from another measurement are valid, especially the having mineral settings currently, the having mineral is stored as the mineralid which is a number unique to a specific classification method and/or grouping so, care should be taken when transferring filtering parameters between measurements to ensure both measurements are using the same classification method and/or grouping technical details shape factor (aspect ratio) the term shape factor is a broad definition of various method to characterize an object's outline feature, and is generally used to get an consistent measure of how rounded the obejct is in the case of the shape factor used for the tmq and seen in the quantifcation result table, the aspect ratio formulaton is being used the formulation of which is in this formulation of the aspect ratio shape factor, the dmin is the shortest orthogonal diameter measured for the grain/particle, while the dmax and the longest orthogonal diameter limitations the current version of the tmq will only provide the elemental concentration, regardless of the compound selected in the espirt quantification recipe it is known that without a full espirt license, amics will not be able to fully interact with the espirt api, especially while using the 64 bit version of amics it is suggested in this case to use tmq only with the 32 bit version of amics example integration with la icp ms one of the key applications of the tmq feature is to integrate the amics large area scan with third party analytical tools, such as secondary ionization mass spectrometry (sims) or laser ablation icp ms (la icp ms) one of the weaknesses of many of these high resolution spot analyses is the difficulty in navigation across the surface of the sample to find the target mineral and so therefore the ability of amics to scan over a large area makes it a perfect tool to augment these other spot chemical analysis tools the first step in implementing this workflow is the need for fiducial points to allow for the translation of the cocoordinateystem from the sem to the third party tool these fiducial points should be physical markings on the same which can be easily found and visible in the sem and the third party tool, such as small engraved points once fiducially points have been added the sample(s) can then be loaded into the amics tool of your choice, and with the beam on and calibrated, the user can use then use the fiducial points feature https //app archbee com/docs/ulnx6skegc8ehmpkog5xe/jyzbwbd89x7suefb9z96n in amics investigator to create reference points to be transferred to third party tools note! to be able to translate the coordinate system from the sem to any third party software or tools, generally, at least two fiducial points are required in the case of amics, currently, a maximum of two points can be created and transferred once these fiducial points have been created, the sample can be measured as per the normal sop, though generally, the most useful application is with particulate sample run via particle mapping mode if the sample is measured in matrix mapping or hyper mapping mode, only the grain level data can be used for filtering in the tmq panel, unless the data has been converted to particles using the particulate feature https //app archbee com/docs/ulnx6skegc8ehmpkog5xe/qd914crcf9eazwrg3svpc following the completion of the analysis of the sample, the tmq panel can then be used to sort and filter target minerals, and quantification of these minerals will provide a rough estimate of the elemental composition the data can then be exported as a text file, and grains/particles of interest can then be selected based on the user's target element(s) the list of grains/particles can then be transferred to third party tools and using the saved fiducial points per sample to align the coordinate systems access requirements a valid license with amics offline or amics online reviewer status comments