README.md

In atusy/qntmap: Enhance quantitative analysis of EPMA map

Enhance quantitative analysis of EPMA maps with qntmap

Overview

This package generates mass concentration maps and phase distribution maps based on X-ray mapping data and spot analysis data from EPMA.

See “How to” for a usage and Yasumoto et al. (2018) for implementations.

Current version supports data from JEOL-style EPMA.

Installation

Copy & paste a following command to R.

source("https://install-github.me/atusy/qntmap")

How to

1. EPMA analysis (spot before map)
2. Export data from EPMA to PC
3. Run qntmap on R for data processing.

Details below.

EPMA analysis

Conversion is performed by utilizing spot analysis data as internal standards. Thus, spot analysis must be done prior to mapping.

Spot analysis

• Analytical conditions
  • Same as those conventionally applied in your lab.
  • Use wavelength-dispersive X-ray spectrometer
• Spots to be analyzed
  • 20 spots per phase in the area to be mapped (the more is better).
  • It is better but not necessary to quantify grains larger than mapping probe diameter.
  • Make sure at least 20 spots per element are analyzing grains larger than mapping probe diameter.
• Identify phases in comment
  • Give same comments on the same phase with the similar compositions.
    • e.g., quartz, plagioclase, garnet-core, garnet-rim, …
  • An alternative is to use external file later.

Mapping

• Analytical conditions
  • Acceralating voltage must be same as that in spot analysis.
  • Probe diameter should be larger than that in spot analysis.
  • Probe current is recommended to be 100 nA following Lanari et al. (2014).
  • Dwell time is recommended to be 0.1 - 0.3 sec following Lanari et al. (2014).

Example of analytical conditions

| | Spot | Map | Comment | |:---------------------|-------:|---------:|:---------------------------------| | Acceralating Voltage | 15 kV | 15 kV | Must be same in spot and map | | Probe diameter | 3 μm | 20 μm | Must be smaller in spot than map | | Probe current | 10 nA | 100 nA | | | Peak dwell | 10 sec | 120 msec | | | Background dwell | 5 sec | NA | No need to analyze in map |

Export data

1. ASCII convert mapping data into matrix format, and save the result in the directory where raw data is stored (e.g., .map/1).
2. Export whole directory of analysis containing .map directory and .qnt directory

Required files

Spot analysis

The exported data are stored in a directory named by .qnt in most environments. If using JXA-8230, a directory’s name is {PROJECT}_{#}_QNT where {PROJECT} is name of a project’s name defined by user or “PROJECT” if undefined, and{#} is a variable integer (e.g., PROJECT_0001_QNT).

| File name | Descriptions | |:---------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | .cnd/elemw.cnd or Pos_001/data001.qnt | Metadata including dwell time for peak and background, and relative positions of backgrounds. In some case, .cnd/elemw.qnt is incomplete or missing, and needs to be prepared manually (e.g., https://gist.github.com/atusy/f1577b67b8874c9e915941c0725d0e22). JXA-8230 lacks .cnd/elemw.cnd, but provides Pos_001/data/qnt. | | bgm.qnt | Minus-side background intensity | | bgp.qnt | Plus-side background intensity | | elem.qnt | Element names specified for matrix corrections (e.g., oxide or metal in ZAF) | | elint.qnt | Element names as is. | | mes.qnt | Probe current | | net.qnt | Net intensity | | peak.qnt | Peak intensity. This file is optional. If missing, peak intensity is calculated from net and background intensities. | | stg.qnt | Coordinates and comments | | wt.qnt | Mass concentrations [wt%] |

Map analysis

The exported data are stored in a directory .map/{#} where {#} is a variable integer in most environments (e.g., .map/1). If using JXA-8230, a directory name is {PROJECT}_{#1}_MAP_{#2}_csv where {PROJECT} is name of a project’s name defined by user or “PROJECT” if undefined, and{#1} and {#2} are variable integers (e.g., PROJECT_0001_MAP_0001_csv).

| File name | Descriptions | |:--------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | *_map.txt or data*.csv | ASCII converted mapping data (e.g., 1_map.txt, 2_map.txt,… or data001.csv, data002.csv, …) | | *.cnd | Analytical conditions: element name, dwell time, probe current, step size, pixel size, and coordinates. File names must corresponds to mapping data (e.g, 1_map.cnd, data001.cnd) |

* indicates wild cards.

Run qntmap on R

For data processing.

Interactive mode

Follow instructions shown by running the following code.

library(qntmap)
qntmap()

As a result, phase identification result is saved in “clustering” directory and mass concentration data as csv files in “qntmap” directory both under the directory contaning mapping data.

Note that interactive mode has limited functions. Use manual mode for full functionality.

Manual mode

A work-flow is available with an example dataset at https://qntmap.atusy.net/articles/qntmap.html .

atusy/qntmap documentation built on April 11, 2021, 4:45 p.m.