1. BL09-MISTRAL DATA treatment flow-chart for soft X-ray cryo-tomography
Normalized and deconvolved tilt series
Conversion from transmission to absorbance
Tilt series manual* alignment
Tomography reconstruction
Segmentation
File from Mistral: name_tomo_norm_deconv.hdf5
Format: hdf5
Approx. size: ~550 Mb
Data processing (BL respon.)
Suggested software**: IMOD, BSoft
From the normalized and aligned tilt series to the 3D reconstruction
Suggested software**: tomo3D
Average size: ~1.5 Gb
Data analysis (user duty)
3D rendering of different region in the reconstructed volume.
Suggested software**: Chimera, Amira.
*At the BL, a fast alignment + reconstruction is done to tackle if the data are worth being manually aligned or not.
**For alignment/reconstruction/segmentation, all the software developed and used for cryo
electron tomography can be used Visualization software: ImageJ.

2. BL09-MISTRAL DATA treatment flow-chart for soft X-ray cryo-tomography
Normalized and deconvolved tilt series
Conversion from transmission to absorbance
Tilt series manual* alignment
Tomography reconstruction
Segmentation
Data processing (BL respon.)
Normalized tilt series
(0 degree image, field of view ≈ 12 μm x 12um)
user duties
Reconstruction
(voxel ≈ 12 nm x 12nm x 12 nm,
estimated resolution 54 nm half pitch)
Aligned tilt series
Segmentation: blue – nucleus, orange - vesicles

3. BL09-MISTRAL DATA treatment flow-chart for spectromicroscopy
Data processing (BL respon.)
File from Mistral: name_specnorm_ali.hdf5
Format: hdf5
Approx. size: ~3.8 Mb for each image (for each energy step).
Typical number of steps: 130 – 180 per absorption edge.
Absorbance energy series
Spectra extraction
Spectra normalization
Spectra interpretation
Suggested software: ImageJ, TXM-Wizard
Data analysis (user duty)

4. BL09-MISTRAL DATA treatment flow-chart for spectromicroscopy
Data processing (BL respon.)
Absorbance μt from MnO2 crystals at 515 eV.
Absorbance energy series
Spectra extraction
Spectra normalization
Spectra interpretation
1 μm
Average O – K edge spectra
μt from selected pixels
Normalized spectra from 0 to 1
user duties
This is a
reference spectra
available in literature!