AMICS 3.2 Release Notes

introduction in amics 3 2 the 3 2 release of amics is an exciting transformation of the amics platform see the section change notes for 3 2 release for details on the new features and functionality included in this release this is the first version of amics to truly embrace a multi sample workflow we believe this has been accomplished without sacrificing the analytical integrity of the original amics concept by ying gu amics takes a unique approach to multi sample analytical workflows by utilizing a batch methodology that can process hundreds of samples without the need to open them this core approach is in two parts multiple measurements can be open at the same time and share reclassification methodologies the number of measurements open is only limited by the computer’s memory apply the method developed on the open screen to a unlimited number of samples using batch processing see the results live to identify the next set of samples to open and directly work with this approach fully utilizes multi thread parallel processing and can scale with computing power this release also includes major improvements to the matching capability with the addition of hierarchical matching, bse limits on matching, and improvements to the processing workflow we think this first step towards a new generation of automated mineralogy will greatly improve workflows and we are happy to have your feedback disclaimer bruker nano gmbh believes the information contained herein is correct and accurate at the time of release bruker nano gmbh reserves the right to make changes without further notice to the product to improve reliability, function, or design bruker nano gmbh does not assume any liability or responsibility arising out of this product, as well as any application or circuits described herein, neither does it convey any license under its patent rights as far as possible, significant changes to product specifications and functionality will be provided in product specific errata sheets, or in new versions of this document customers are encouraged to check the bruker website for the most recent updates on products trademarks all trademarks, registered trademarks, and product names are the sole property of their respective owners this document and the information contained herein is the subject of copyright and intellectual property rights under international convention all rights reserved no part of this document may be reproduced, stored in a retrieval system, or transmitted in any form by any means, electronic, mechanical or optical, in whole or in part, without the prior written permission of bruker nano gmbh copyright © 2021 bruker nano gmbh life support policy these products are not designed for use in life support appliances, devices, or systems where malfunction of these products can reasonably be expected to result in personal injury bruker nano gmbh customers using or selling these products for use in such applications do so at their own risk and agree to fully indemnify bruker nano gmbh for any damages resulting from such improper use or sale change notes for amics 3 2 changes and new features platform m4 tornado is an option at install this option will install a version of investigator designed to streamline data collection on the m4 including a simplified interface in investigator and m4 specific standards the standard manager has been incorporated into process this major change was introduced to improve workflows and facilitate multi sample workflows the look and feel of the user interface have been updated with bruker colors and logos investigator (sem) improved standard collection mode – checks are performed to avoid collecting phases from boundary phases, and the collected standards are compared against current global and user lists to assign a label to the spectrum if possible changed the amics user interface to have a bruker theme added a “key mineral” feature – the user can define separate segmentation parameters – one set for specially selected mineral/s and another for the remainder of the phases added the ability to add labels to measurements to capture more information added the ability to record and display brightness/contrast settings during the measurement added the ability to measure a sample as a perfect circle area the system only keeps information within the red measurement area – that is the entire frame will not be measured if cut by the selected circle shape added additional information to the mineral standards for better quality control the system now records the kv used to collect a standard as well as stage rotation settings added the ability to do multi focal measurement, measurement can compensate for samples that are not entirely flat (± 2mm) added the ability to collect x ray based on target count rather than setting a fixed acquisition time added the ability to monitor the bse stability during measurements and to compensate for any changes that might occur due to instrument instability or poor room temperature control bse stability can be set based on relative changes to bse, a bse standard, or based on a set mineral standard (e g quartz) added the ability to terminate measurements based on a set time ability to capture second channel for image, for example se image or cl image, depends on the available detector installed system can be configured to send an email upon fault that stops a measurement, if significant bse drift occurs, or with measurement status updates notifications include detection of a blown filament on tungsten systems a “project folder” can be assigned and all measurements saved in that folder it can setup separately of each sample new measurement name templet includes timestamp addition of a sample holder layout tab and more tools for custom sample holder creation the measurement will stop when a filament fault is detected measurements can be sorted by user selected column beam calibration ability investigator (xrf) improved the reliability of running amics measurements on the m4 tornado platform simplified user interface for m4 systems with ability to set excitation parameters additional information captured and displayed for m4 systems converts to a mre file on the fly ability to capture video channel during m4 data collection data collection in m4 mode is no longer based on frames, allowing the entire measurement to be opened in the esptit for m4 autofocus option for m4 and the ability to set the focus for a measurement and record data, empowering several measurement areas with different focuses to be collected in the same run calculates the total number of datapoints and the total measurement time in m4 record and control high tension and current if needed process major improvements to the ability to work on more than one sample at the same time two new windows have been added with functionality related to cross measurement data reduction the current mineral groupings window is the “key” for the active measurement and can be used to change the display options by changing the colour or the groupings the method window is governed by the oretype and is shared with all open measurements or is the source for the new batch reclassification this area has tabs for mineral standards (where new mineral standards are populated and can be matched or edited), reclassification steps (generated in spectrum tree), and mineral groupings amics now shares the oretype across all open instances of amics, allowing changes in the mineral list or classification steps to be propagated across all open measurements oretypes can be synchronized between open windows automatically or on command new mineral standards may be appended to and oretype within process ability to merge multiple measurements ability compare oretype from an older measurement to the new oretype and rectify changes added a batch process function that can re processes an large number of files in batch major functionality batch files, lists of measurements to reprocess in a batch, are made within the batch the user can select the oretype and groupings to apply to all measurements the batch process gives a live report of progress, including reporting on the area percentage of unknowns and other user selectable mineral phases batch process can be run without a measurement open added exports of new open source and image file formats including ability to export raw data as sqlite and processed data as sqlite and json open source formats can be exported in batch process mode with selectable parameters new text export options for total x ray improved the image export function to include original resolution export for large measurements for image export with bse underlay for rare phase search results, changed the result to include all bse frames particle images are now optionally included in the mdb export major improvements to the sample viewer and groupings including improved the automatic stitching functionality, the ability to view secondary images (e g cl in sem or video in m4), improved transparency options, and the ability to view elemental distribution on m4 images, improved mineral flagging feature, so that it is more visible to the user, addition of bookmarks generate a “psudobse” image from total x ray counts for m4 maps and view this map as a background image bse stability can be toggled on and off in process bse can also be standardized based on a selected mineral phase added the ability to create mineral grouping automatically improved functionality and features for matching include allow users to have more than 256 minerals for display and calculation, and handle the limitation only in calculations with having an auto group feature to reduce the number of entries to an acceptable number (i e <256) the addition of hierarchical groups (high, standard, and low priority) of mineral standards each group is matched in order at different reliability factors minerals matched in higher priority groups cannot be reassigned by lower priority groups matches can now be restricted by a bse range in the mineral standard users can specify a minimum and maximum bse if outside this range the mineral will not match to the standard, regardless of the spectral similarity the bse is calculated based on the average segment bse, allowing for the capture of bse texture of the entire segment for a selected point the “next closest match” is displayed major improvements to calculation, tables, and charts include added liberation by free surface calculation, the ability to do calculations in batch, optional colour column into the modal calculation table, ability to customize liberation and size classes, option to show calculated charts in 2d or 3d algorithms have been modified to improve the association calculation for block mode measurements specified mineral phases can be excluded from calculations ability to export the currently selected calculation to microsoft excel zeros can now be turned off in the mineral association table the mineral standard manager has bene fully incorporated into process, bringing major new functionality into process, including some items in the mineral standard can now be changed without reclassification, including quick touch up, and editing mineral properties highlight and copy global list properties standards in the mineral manager can be viewed and edited without a measurement open it is now possible to automatically generate 2 phase mixes from two or more selected end members each selected phase will generate binary mixes with every other selected endmember three phases mixes can now be automatically generated import multiple spectra at once major improvements to functionality related to particles, touch up and background, including the addition of a detailed particle table to add more capability to sort and explore particle details and added the ability to perform touch up on un x rayed segments a meq (major element quantification) workbench the meq workbench enables the filtering of particles based on user selected criteria, the quantification of selected phases, and the exportation of this quantified information and x y location lists improvements to existing functionality include the ability to clean up small particles after measurement and processing and the addition of a grid directory to help navigate long particle grids added ability to select one or more phases to convert to background and convert block maps to particle maps, a process we call particulization this adds all the functionality of particle calculations to m4 maps improved porosity clean up function added functionality to reversibly convert selected mineral phases to porosity or background major improvements to the functionality of spectrum tree including the ability to multi select clusters to be able to assign/un assign selected clusters as a group, view the spectrum for the current assigned standard in a cluster, range ratio criterion ability to select multi select clusters and add them as new standard entries simultaneously and other new features do classification with bse range show mineral standard list grid show the result xray bse range info show the result mineral trend info edit mineral standards without reclassification tool added the following functions when opening a mre file in tools added a bse histogram added an x ray grey level histogram for any selected mineral based on the grey level recorded at the x ray point that will show the variance in bse for that mineral added an x ray grey level histogram for any selected mineral based on the grey level recorded at the x ray point but also taking the area of the segment into consideration added a classification reliability chart for a selected mineral (only available for measurements measured with vs3) added the mineral trend added a split view (like the option in process) ability to view bse, segmented/classified and image overview all in one view added an interface to assist with creating a sample holder fixed bugs investigator fixed memory leaks in investigator fixed memory leaks when using key mineral analysis feature resolved issues with running long measurements through investigator on the m4 tornado fixed the software crash that occurred when clicking on the results tab while the system is busy measuring resolved several stage movements issues with various sems resolved issue where log file data was missing when collecting in matrix mapping mode resolved various issues related to brightness and contrast settings, investigator can now automatically idneify major brightness and contrast issues and restart the esprit api measurements run in rotation order regardless of sample number process fixed the software crash that occurred when clicking on other tabs while the system is busy calculating fixed the crash when clicking tree info in the spectrum tree context menu for the micro xrf, rectified an issue with opening version 2 x generated files with the new version 3 x build fixed the issue that when selecting multiple minerals and then select export image, the image would only show one of the selected minerals repaired the corruption of the calculation cache after a batch run generating mixed spectra no longer generates duplicated mineral ids made the scale presentation when using area criteria in spectrum tree more clear removed the blank spaces at the end of cells in the particle grid tab better utilization of “expand” and collapse” options in the software fixed issues with progress window being hidden behind active windows known bugs and issues elemental distribution view is currently limited to m4 maps, and the user must select the elements based on amics channels this is a feature in beta and under continuing development minor bugs around duplication of oretype and working with some shared oretypes