# Soft X-ray Microscopy Techniques for Medical and Biological Imaging at TwinMic--[PERSON]
## 2 Materials and Methods
### TwinMic Imaging Modes
#### 2.1.3 Ptychography and Coherent Diffraction Imaging (CDI)  
Ptychography [58; 59] is an emerging scanning imaging technique based on CDI [60; 61; 62; 63]. It is attracting interest at synchrotron facilities, as it provides not only transmission imaging data, such as STXM, but also phase information simultaneously. The technique provides  
Figure 3: Schematic view of the TwinMic full field imaging mode setup, with a condenser ZP (CZP) illuminating the specimen (S), an order-selecting aperture (OSA), and a micro zone plate (MZP) that magnifies the image of the specimen into the detector with a directly illuminated CCD camera.  
very high resolution over large sample areas and is characterized by the high reliance on computationally demanding techniques for the reconstruction of the results.  
The single image (probe) is a diffraction image that, via numerical inversion, can provide us with the original transmission image in terms of intensity and phase. This is a complex mathematical problem with multiple solutions. To obtain the right solution, the sample is scanned at a step size smaller than the probe size, ensuring adequate overlapping of subsequent illuminated areas, acquiring a diffraction pattern for each step in the raster scan. Indeed, the redundant information due to the oversampling allows computer algorithms to reconstruct reliably both the sample transmission function and the illuminating probe, recovering the amplitude and phase of both these signals. As in classical SXTM, by reconstructing a stack of images acquired at photon energies across the absorption edge of a specific chemical element, ptychography allows for XANES-type studies, as demonstrated in [64; 65], providing sub-micrometric resolution chemical speciation.  
In addition to ptychography experiments, the beamline has successfully tested the keyhole-CDI technique [61], which, by being a single-shot technique, is, in general, preferable for in situ dynamic studies, such as monitoring the dynamics of electrodeposition [64; 65], but which can also be used for biological samples [66].  
Figure 4 outlines the direct-detection transmission X-ray ptychography setup at Twin-Mic, where ZP optics illuminates an area over a sample placed at a certain distance from the focus, while the sample is raster-scanned with a step size smaller than the probe size. Currently, the same previously mentioned back-illuminated Princeton CCD camera used for TXM is also employed for ptychography.  
Ptychography can be classified as a computational technique as it requires reconstruction similar to that of a computed tomography workflow. Advances in algorithms and computational resources have affected the quality and speed of reconstruction. TwinMic, in collaboration with the Elettra Scientific Computing group, has developed a specialized data acquisition and ptychographic reconstruction in-house software called SciComPty that allows for the state-of-the-art reconstruction and optimization of various experimental parameters. SciComPty [67] was developed and tested with data at energy ranges suitable for medical and biological studies. The system and the in-house computing expertise should allow noncomputational researchers to employ this technique for an easier absorption and phase imaging data analysis.  
Figure 4: Schematic view of the TwinMic ptychography setup with the zone plate (ZP), the order-selecting aperture (OSA), the specimen (S), and the CCD camera.