Spectrum Tree Tab

spectrum tree is a unique tool developed for amics, making use of the availability of the spectra data from an amics data acquisition when the spectrum tree tab is selected the initial window will only contain a greyed area in the middle of the main window (see example image below) for the spectrum tree, the main active area is the main spectra view area, which will be where the user will interface with selected spectra once spectra have been selected the user can cycle through the selected spectra by using the up and down arrows to select the input spectra, there is a tree input parameter at the top of the right hand panel, and use the drop down menu labeled data source the drop down menu will give the following data source options randomset this option will select a random subset of spectra from the total collected spectra data sets \<all> this option will select all the spectra collected selection assuming a subset of segment/grains/particles were selected in the sample image or particle grid tabs, this option will select all the spectra associated with the selected segments/grains/particles screen this option will select all the spectra left on the screen in the sample image tab screen unknown this option will select all spectra on the screen in the sample image that were classified as unknown frame this will select all spectra from a single selected field (usually from a matrix mapping dataset) all unknown this option will select all spectra classified as unknown in the sample from minerals this option will open a new pop up window allowing the user to select materials from the classification method used to measure the specimen and select all spectra matching the selected classifications the final menu used for the specimen tree is the main clustering menu section in the right hand panel this section provides access to the different clustering options which can be applied to the selected spectra details on the various binning criteria available, and how to make use of these options can be found in the https //help amics info/spectrum tree methods once the user has implemented a tree cluster, any resultant spectra batch can be assigned to another material classification this can be done by using the classify as option which will open a drop down menu containing all the material classes in the classification method used for this specimen the assignment of the selected batch of spectra will only happen after clicking the assign button note assigning the branch to a material class in the spectrum tree will not make any changes current sample results to force the assignment of the spectrum tree branch to the current sample right clicking the assigned branch, and selecting assign cluster will force the change to the current specimen classification to allow further interrogation of the result of the tree branches spectra there is also the option to quantify the spectra from a selected branch, by clicking the quant tree item option, and the quant now! button selecting this option will open a new pop up window (shown below) which allows for different quantification options these options are quant avg spectrum this option will sum up all the selected spectra and find the average value for the whole spectra to send for quantification quant max spectrum this option will find the highest count for each channel and send a spectrum with these highest count values quant other spectrum this will enable additional options, which will remain greyed out until this option is selected quantify all xrays selecting this option will disable the number to the right of this check box, and will quantify all the selected spectra if this is unchecked, then it will quantify the number of spectra set by the user in the text box to the right of the menu combined xrays by counts this option will add spectra from the selected spectra until a total count of the summed spectra reaches the value set by the user on the right note! selecting combined xrays by counts will disable the previous option to select the number of spectra therefore if selected more spectra than entered into the pervious text box could be quantified for the quantification to work bruker esprit must be running already, as amics will not open it automatically access requirements a valid license with amics offline or amics online