Open and process 3D datasets generated by TESCAN FERA Xe plasma FIB-SEM with ToF-SIMS microscopes
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 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 remi.branco@hotmail.fr or daniel.thomas.oldfield@gmail.com 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
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