Skip to main content
SIMS (Secondary Ion Mass Spectrometry) analysis parses depth profile data from Excel workbooks or delimited text files, extracting concentration-vs-depth curves for each detected ionic species. The pipeline automatically identifies depth and species columns, detects measurement units from column headers, and produces aligned depth profile arrays.

​
Overview

The SIMS pipeline processes data in three stages:
  1. File reading: for Excel files, locates the correct worksheet by looking for a “Processed data” sheet or falling back to the first sheet with numeric data. For text files, finds the header row and skips any instrument preamble
  2. Column identification: pattern-based matching separates the depth column from species concentration columns, and detects units from the column headers
  3. Data extraction: produces aligned depth and concentration arrays for each species, with metadata recording the species detected and units used

​
Key Metrics

​
Adding Data

Upload depth profile data as Excel workbooks (.xlsx or .xls) or as delimited text (.txt, .csv, or .dat, separated by tabs, commas, or semicolons) through the data page. Processing starts automatically once the upload completes.The pipeline expects a worksheet with a depth column and one or more numeric columns for species concentrations. Column headers should include unit information (e.g., “Depth (nm)”, “Si (at/cm³)”) for automatic unit detection.

​
Viewing Results

SIMS results aren’t displayed in the Atomscale app; the data item page shows “This file cannot be analyzed but is stored.” Once processing completes, retrieve the depth profiles through the API: Get SIMS Data returns one depth-concentration profile per detected species, and Get SIMS Species Profile returns the profile for a single species.
If the automatic unit detection picks the wrong units, you can override depth and concentration units in the pipeline inputs (depth_units, concentration_units) when you re-run analysis through the API.