autopew is designed for arbitrary translation between planar/2D Cartesian coordinate systems using affine transforms and human-in-the-loop workflows.

This is applied to integrating coordinate systems across analytical instrumentation, with each instrument typically having its own individual coordinate systems based on imagery and/or a sample stage. autopew also includes functions for importing and exporting files, for automated generation of point sets within a relevant format for each piece of analytical instrumentation. autopew outputs currently included a .scancsv file which can be directly imported into Chromium laser ablation navigation software.

Why use autopew

autopew is designed for easy referencing between analytical equipment and/or images. This allows the time spend on analytical equipment to be more effectively used for data collection rather than spending valuable time locating the areas of interest.

This software also allows for tracking of the context of in-situ microanalysis by allowing reference to large images and areas which will allow for new insights into what effects chemistry of given particles with reference to their location and micro-environment. We can then track the analysis between different analytical equipment and make inferences on macroscale processes from well characterised in-situ microanalysis [1].

Although primarily designed for use of laser ablation analysis on geological material this software can be used for any microanalytical technique, including electron microprobe analysis, x-ray fluorescence mapping, scanning electron microscopy and ion beam analysis.

See also

For outlined examples of how autopew is used, see Examples

What is autopew not?

  • Not currently capable of 3D affine transforms (i.e. no ‘focus’ attribute).

The current development plan for autopew can be found here.


This documentation is a work in progress and is updated regularly. Contact the maintainers with any specific questions/requests.


[1]Pearce, M. A., Godel, B. M., Fisher, L. A., Schoneveld, L. E., Cleverly, J. S., Oliver, N. H. S., and Nugus, M. (2017). Microscale data to macroscale processes: a review of microcharacterization applied to mineral systems: Geological Society, London, Special Publications,, v. 453 doi: 10.1144/SP453.3.