A web Database for electron Microprobe Analyses to assist EMP lab managers and users

Transcription

1 A web Database for electron Microprobe Analyses to assist EMP lab managers and users Department of Geological Sciences University of Colorado Boulder Boulder CO (USA)

2 Introduction Lab managers and users of electron microprobe (EMP) facilities require comprehensive, yet flexible documentation structures, as well as an efficient scheduling mechanism. A single on-line database system for managing reservations and providing information on standards, quantitative and qualitative setups (element mapping, etc.), and X-ray data has been developed for this purpose. This system is particularly useful in multi-user facilities where experience ranges from beginners to the highly experienced. New users and occasional facility users will find these tools extremely useful in developing and maintaining high quality, reproducible, and efficient analyses. Page 1

3 Concept and installation This user-friendly database is available through the web, and uses MySQL as a database and PHP/HTML as script language (dynamic website). The database includes several tables for standards information, X-ray lines, X-ray element mapping, PHA, element setups, and agenda. It is configurable for up to five different EMPs in a single lab, each of them having up to five spectrometers and as many diffraction crystals as required. The installation must be done on a web server supporting PHP/MySQL, although installation on a personal computer is possible using third-party freeware to create a local Apache server, and to enable PHP/MySQL. The installation of this database is made easy and knowledge of HTML, PHP, or MySQL is unnecessary to install, configure, manage, or use it. Since it is web-based, any user outside the EMP lab can access this database anytime through any web browser and on any operating system (Fig. 1 - next page). The access can be secured using a general password protection (e.g. htaccess). Page 2

4 Server Int d ta e ern s s dre se on ge) p s a Re L p M T (H Internet Server DATABASE Access script, HTML translation SCRIPT Database query, return value(s) Google server room in Lenoir, NC Photo credit Google Client (user) Fig. 1: Working scheme. Once installed on a PHP-MySQL server, any operating system (Windows, Mac, Linux) and any browser (with javascript enabled) can access the database through the Internet. The database can also be installed on a local computer using an Apache-PHP-MySQL package (e.g. EasyPHP, MAMP, LAMP...). Page 3

5 The web interface consists of 6 main menus: Page 4

6 1 Standards : List of standard defined in the database, including detailed information (e.g. material type, name, reference, comments, and analyses). Images such as EDS spectra or BSE can be associated with a standard. Page 5

7 1 Standards :...Search option includes search by standard name, by element present in the standard, and/or defined as an element for standardization. Page 6

8 2 Analyses : Typical setups to use for quantitative analyses, calculation of mineral composition based on a mineral formula... Page 7

9 2 Analyses :...calculation of mineral formula based on a fixed amount of oxygen, or of cations (using an analysis in element or oxide weight-%) is also possible. This option includes re-calculation of H2O and/or CO2 based on stoichiometry, and oxygen correction for F and Cl. Another option offers a list of any available standards and possible peak or background interferences for a series of elements. Page 8

10 3 X-ray maps : List of different setups recommended for element mapping using WDS, and a map calculator to facilitate map setups and to estimate the total mapping time. Another feature lets you upload existing images and, after calibration, lists the stage position based on a twopoint fiducial calibration. Page 9

11 4 X-ray data : Complete database of x-ray lines for all elements (K, L, M, absorption edges, and satellite peaks). Search can be made for a specific element, a range of energy (kev), or wavelength. Page 10

12 4 X-ray data : A check for possible interferences on peak or background is also possible. Theoretical x-ray peak positions for each crystal are calculated based on the 2d spacing of each crystal and the wavelength of each line*. * Including correction for crystal refraction (k) using the modified Bragg s law: nλ = 2d(1-k/n2)sinθ Page 11

13 5 Agenda : Displays the reservation dates for each month and for each EMP lab defined. It also offers a reservation request option, this request being sent by to the EMP manager for approval. Mouse over a date to see additional information; some details are only visible by the administrator. Once a user request a reservation, an is automatically sent to the user, as also to the microprobe manager for review. A warning is triggered for reservation made over holiday period or when the lab manager is unavailable (based on a list of holiday and vacation days in a text file). Page 12

14 6 Admin : Password restricted area of the database containing all necessary options to manage the database through userfriendly forms: standards, analysis labels, x-ray map setups, element and PHA setups, agenda entry, modification of your profile, creation of new access to the administration section, backup of the database... You can also access the database using PhpMyAdmin, although the use of this tool is not advised (risk of breaking link between tables...). Page 13

15 Some extras! The Home menu also contains an About the EMP... submenu, which lists the parameters of your microprobe (from the preferences file that you create), a contact form to send to the webmaster or the lab manager, and also an option to change the main color of the website, the font and the background image. You can also add two URLs, one for your lab webpage and another one for your department. In addition, a simple print button in the main menu lets you print a page without the problem of formatting... You want more? You have ideas? Contact Julien to suggest updates or improvements! Interested in a demonstration? Visit one of the following websites (admin access: guest / agu12)... JEOL JXA CAMECA SX-50 & SX-100 (Link will be active after December 2nd) Page 14