SoftXMed: Soft X-ray spectromicroscopy for medical tissue samples

About the project

SoftXMed-project (Soft X-ray spectromicroscopy for medical tissue samples) is an interdisciplinary project combining teams with background in physics, biochemistry and medical sciences. The aim of the project is to characterise abnormalities in different patient-derived tissue samples using scanning transmission soft X-ray microscopy (STXM). The technique is novel in this context, but its feasibility has been demonstrated during the preliminary experiments carried out by the team using samples prepared for transmission electron microscopy (TEM). Complementary imaging and spectroscopic techniques are essential to validate the findings of STXM, and thus the project heavily utilises also “in-house” techniques from TEM to light microscopy.

Tissue samples (from human and mouse models) selected for this project present well-characterised known diseases (e.g. storage diseases) as well as newly found diseases whose pathomechanisms are still unknown. Using the know diseases as a “reference” to validate our approach, the characterisation of the new diseases with novel imaging techniques may help to e.g. develop diagnostic techniques for these diseases and learn from their disease mechanisms.


The project combines expertise and techniques of spectroscopy, microscopy, biomedicine and biophysics, and thus active collaboration with different in-house and international groups is needed. The key players in Oulu are listed here:

Minna Patanen (Docent, PhD in physics) belongs to a NANOMO research unit ( (Faculty of Science). She coordinates the project and is responsible for the STXM imaging experiments and data analysis. Her researcher profile can be found at:

Ilkka Miinalainen (PhD in biochemistry) is a coordinator of the Electron Microscopy (EM) Biocenter core facility ( He supervises the electron microscopy and sample preparation. His contact information can be found at:

Salla Kangas (PhD in medicine) carries out research in Uusimaa-Hinttala group ( in the PEDEGO research unit related to neurological and multiorgan diseases in children. She is an expert of multitude of techniques related to revealing pathomechanisms and signalling pathways in these diseases at cellular and molecular level. Her researcher profile can be found at:

About the technique

STXM is a technique which utilises electromagnetic radiation in soft X-ray energy regime to irradiate the samples, and collects the transmitted light. Soft X-rays are used because this radiation has suitable energy to cause excitations of inner-shell electrons in atoms. The energy of the radiation has to be exactly matching the energy difference between the so-called ground state and excited state in order the core-excitation to happen. Each element has its own characteristic energies at which these excitations can take place, furthermore, the energies of the excitations are modified when the atom interacts with its neighbours (i.e. forms chemical bonds). Thus, in the heart of the STXM technique is to continuously tune the energy of the radiation to locate these excited states in the specific sample in question: this energy will give information about the chemical substances present in the sample. The size of the irradiating beam is very small, less than 50 nm, which means that the sample can be studied with a spatial resolution of < 50 nm. In practice, the sample is place on a scanning stage, and a raster scanned image of the sample can be formed at each energy. Compared to transmission microscopies in which only one energy of radiation is used, STXM is like a colour photos compared to black and with photographs. The spectral information provided by STXM may help to identify unknown substances that seem to accumulate inside the cells, and thus find possible biomarkers of diseases.

STXM can be carried out at synchrotron radiation facilities, and the team is a long-term user of these large-scale infrastructures in Sweden, France and Japan. The technique itself is still evolving and a lot of progress is foreseen regarding e.g. sample preparation techniques and sample environments. As the STXM itself would not require ultra-high vacuum conditions, conductive or stained samples, the aim is also to investigate possibilities for less processed samples.

Last updated: 9.4.2018