Materials Library

version requires amics 5 1 0 or newer the released version of amics is {{version}} and can be found at docid\ se8jyhxszdqfpit7s1ja0 with instruction on the docid\ e1faehd1k20uedqhptzlx page manuals for previous versions of the software can be found at the docid\ d2biwe sybowhhdww0anz page materials in amics materials are defined as solids with defined chemical and spectral characteristics we deliberately use the word "materials" even though most of our users are analyzing minerals materials is a more general term, and thus is more inclusive of all users it is also not entirely proper to say that we can identify minerals, since we do not measure the crystallin structure we can only analyze some chemical characteristics that allow us to identify the material with a degree of confidence, even when they are earth materials the material library is managed from the "references" tab this can be accessed even without an experiment open in investigator, but still requires an open experiment in process each entry can be considered to have a "material definition" consisting of the name and chemical properties of the material and a one or more "reference spectra" that is a representative spectrum used in matching in previous generation of amics this was called a "standard " we have changed this nomenclature because they are not "standards" in the scientific sense, but rather a phase in a model of a natural or material system the original philosophy of amics, from ying, was that you start with a observation the spectrum from the specimen and build out it's characteristics thus a 1 1 relationship always existed between the reference spectrum and the material it defined however, in amics 5 we have attempted to give more flexibility in the way the classification workflow is constructed this has resulted in several major changes we think will make the system easier to use, particularly while exporting new projects a single material definition can now have several sub definitions each sub definition can have unique chemistry or be assigned the master chemistry only the master name and color are shown on the results list this allows sub definitions to accommodate situations where a variation in beam or sample resulted in slightly different reference spectrum without a different in the resulting classification reference spectra can be disabled in a material definition this allows a material definition to be a "holder" for assignments that may only come from spectrum tree steps or touch up steps a material definition can be added directly from the global library or from the user library this allows the list to be developed before analyzing the specimen the global list has entries with simulated spectra while the user list has material deifications from all methods on the system material definitions amics uses a library of reference materials, which contains one or more spectrum, to classify measurement data each reference material library contains a list of materials, as well as grouping data for the material list and any processing steps (touch up and spectrum tree) the user must build this list and define the chemical and spectral characteristics of the material to classify it the material workflow is stored on the computer that it was made and within each measurement at the time of classification the reference tab's main window will show an image of the selected reference spectrum, and is interactive hovering over the spectrum window will bring up the line energy where the mouse pointer is required information in previous version of amics each material is required to have three properties a name the name must be unique within the classification method a defined chemical formula, density, and elemental composition the elemental composition must equal 100% a reference spectra however, in amics 5, materials can miss one or all of these properties however, without these properties , the material will not calculate correctly or will not be used for matching, if no spectra is assigned to the material the material definition characteristics can be accessed in the "property" window if the material definition is missing any of the required information it is still possible to classify with the entry in the workflow however, the results may be invalid invalid material definitions are indicated in the material list with a caution icon if they are missing elemental or density information a minus sign is shown if it is missing a reference spectra elemental data the elemental composition, along with average atomic number and density, are used in calculations they must be entered correctly for the calculations to be an accurate model of the mineral or material they are listed in the "property window" to the right hand of the screen make sure the "classification" icon is active to edit any values the values can be viewed in "current results" but cannot be edited elemental values can be derived from several sources the global mineral database has the elemental compositions, density, and formula for thousands of minerals add them to a material definition by selecting the material definition with the "classification" tab active, right click on the global list entry, and select "copy data" or "copy data and name " it is also possible to add an entire entry, including the simulated reference spectra, by selecting "insert " the elemental data can also be added manually use the "add element" button to add an entry and define the chemistry add each element one at a time the elemental values must equal 100%, and the "normalize elements" (100 and elemental symbol) button has been added to help use the "formula parser" (xyz and elemental symbol) to automatically generate a chemical formula for the entry reference spectra (see next section) can also be quantified if bruker esprit is installed to access this function right click a material definition in the classification tab and select "quantify reference material " the resulting values can be saved back to the material definition special definitions the system will automatically generate special materials in the method they will be shown on the current results and do not need to be added to the method unknowns any segment that has not been classified pores segments that have been identified as "background" but are within a particle only generated on partialized measurements low counts segments where the count rate is below a threshold this is set in the settings they will not be classified un x rayed segments that were identified as material, but no x ray point was placed this typically occurs because of a small segment filter being applied at the time of measurement reference spectra note the number with a brown background represents the energy line where the mouse pointer is located the text with the blue backgrounds represents the element closest to the energy line, with the number representing the different in the peak of the indicated element versus the highlighted energy line (i e brown background) underneath the main spectrum viewing window is the material search interface, which allows for the currently selected spectrum to be compared to either a 3rd party list of reference spectra, or spectra from all material libraries on the system it is possible to compare the selected spectrum against saved spectrum by checking either clicking the compare to database the reference spectra is used for matching amics uses a whole spectrum best match algorithm for this to work, it is best to have reference spectra to match to that are collected from the sem that the system will be measured on however, amics has several ways to add reference spectra! in order of quality they are directly use amics process or amics investigator to collect point data from a known location for example, from a standard, a position on a specimen that is a known material, or from a sample that has been measured in epma it is also possible to collect with a 3rd party software and import into amics for example, use bruker esprit to collect long count data use the spectrum tree to find and generate a high quality sum spectra the spectrum tree can have a source set for unknowns and has functions to help identify pure spectra use "seed search" to select an unknown and search the entire measurement for similar unknowns that can be combined to make a single reference spectra select one ore more unknowns and add them to the workflow as a add simulated spectra to the workflow this can be done by right clicking the spectra form the global library and selecting "insert"