Project description

Why TOF-SIMS ?

We needed a convenient way to explore the 3D datasets generated by a TESCAN FERA Xe plasma FIB-SEM with ToF-SIMS. This notebook expands on the functions provided by the manufacturer.

Highlights

Plots

Available functions so far:

Read data from TOF-SIMS (.HDF5) files, making the data directly accessible in Python (numpy/pandas/matplotlib).
Generate top, sides projections, visualise surface before FIB-ing
Plot detected masses
Maximal projections for any given axis (x,y,z) and every isotopes/masses (useful to have a quick look at detected species).
Inspect top, side and depth projections for a given isotope/mass
Plot (and superpose) the abundance of species over any axis.
Overlays maximal projections.
Read in the complete file header. Get access to every setting of the machine recorded at the time of the experiment.
Export plots.
3D interactive plot

Machine learning

Multivariate analysis with PCA, kPCA, IPCA
Machine learning (KMeans)
Detailed cluster analysis

Instructions

Code in TOF-SIMS Notebook.ipynb should be self-explanatory. If needed feel free to contact us at remi.branco@hotmail.fr or daniel.thomas.oldfield@gmail.com Help and feedback is very welcome.