TOF-SIMS 1.1.0

Open and process 3D datasets generated by TESCAN FERA Xe plasma FIB-SEM with ToF-SIMS microscopes

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 package expands on the functions provided by the manufacturer.

Highlights

Machine learning

• Multivariate analysis with PCA, kPCA, IPCA
• t-SNE clustering
• Machine learning (KMeans)
• Detailed cluster analysis

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

Instructions

Code in TOF-SIMS Notebook.ipynb should be self-explanatory. If needed feel free to contact us at [e-mail] or [e-mail] Help and feedback is very welcome.

What's next

• More machine learning (DB-scan)
• Better 3D plots (open3D)
• Data reprocessing/peak-refining
• Peak identification
• Denoising with neural network