… based on our new analysis method, we were able to show the number of nucleosomes in each nanofocus that could allow us to define the possible chromatin structure and the nucleosome density around the break sites. This method is one of the first demonstration of a single-cell based quantitative measurement of a discrete repair focus, which could provide new opportunities to categorize spatial organization of nanofoci by parametric determination of topological similarity.Read more
Quantification of DNA damage induced repair focus formation via super-resolution dSTORM localization microscopy
We have released the latest version (v2.1.3) of TestSTORM. Here are the changes:
- Significant memory reduction for the simulations (should be between 2 and 4 times).
- Performance improvement when running the simulation with large number of labels.
- Axial position for the “Array” pattern now can be set in the GUI. It is useful for generating calibration files for the astigmatic 3D simulations.
- Some minor fixes for v2.1.1
Also we backported a minor feature from the development branch and released rainSTORM v3.1.7. Here are the changes:
- Backport ExportBoxTracker tool to export localization data from selected ROIs on the Super-Resolution Image.
- Updated Auto Drift Algorithm with comments.
- Removed the BaSDI Drift Correction button from the GUI, as the implementation wasn’t as good as expected.
Poster Session 2 (Tuesday, April 16, 17.50–19.05):
- P2-A/10 Multimodal Localization Microscopy with Efficient Photon Collection – T. Gajdos, Zs. Cserteg, Sz. Szikora, J. Mihály, B. B. H. Kovács, T. Novák, M. Erdélyi (University of Szeged, Hungary)
- P2-C/12 Quantification of DNA Double-Strand Breaks via STORM Localization Microscopy – D. Varga, H. Majoros, Zs. Újfaludi, T. Pankotai, M. Erdélyi (University of Szeged, Hungary)
We have initiated an annual meeting for super-resoultion microscope users in Hungary. The first symposium will take place at University of Szeged, on 8th March 2019.
The preliminary program is built around the major super-resolution techniques and their applications. After the talks the participants can visit multiple microscope laboratories in Szeged. Bring your own samples!
Super-resolution localization microscopy provides a powerful tool to study biochemical mechanisms at single molecule level. Although the lateral position of the fluorescent dye molecules can be determined routinely with high precision, measurement of other modalities such as 3D and multicolor without the degradation of the original super-resolved image is still in the focus. In this paper a dual-objective multimodal single molecule localization microscopy (SMLM) technique has been developed, optimized and tested. The proposed optical arrangement can be implemented onto a conventional inverted microscope without serious system modification. Read more
- Replaced Matlab’s iteration to a custom one for increased reliability when calculating scalar or vectorial PSFs.
- Modification to the focal position determination when calculating scalar or vectorial PSFs. Results only slightly different focal position than the previous algorithm, in normal cases (~22 nm difference with the default settings).
- Fixed a bug when calculating scalar or vectorial PSFs (not sure whether a new Matlab version caused it or it was originally in the code). The PSFs shapes and peaks were only marginally affected.
- Made a workaround for a bug causing higher blinking event brightness when simulating with very low “Sample depth” value.
- Added “Synaptosomes” option to the random “Vesicles” pattern.
- Parameters files exported with previous TestSTORM versions (2.0.x) and containing “Rods”, “Vesicles” or “Octagons” patterns can not be imported any longer starting this version.
- Added a tool with which the generated PSF can be depicted.
Other clean-ups and modification in the code which should not affect the behaviour of the program.
Tamás Gajdos won a grant at the National Talent Program (Nemzeti Tehetség Program). He will cover the MBFT XVII. Congress registration fee, a german language course and an IT upgrade by this grant.
TestSTORM: Versatile simulator software for multimodal super-resolution localization fluorescence microscopy
Optimization of sample, imaging and data processing parameters is an essential task in localization based super-resolution microscopy, where the final image quality strongly depends on the imaging of single isolated fluorescent molecules. A computational solution that uses a simulator software for the generation of test data stacks was proposed, developed and tested. The implemented advanced physical models such as scalar and vector based point spread functions, polarization sensitive detection, drift, spectral crosstalk, structured background etc., made the simulation results more realistic and helped us interpret the final super-resolved images and distinguish between real structures and imaging artefacts.
Novák et al., Scientific Reports 7, Article number: 951 (2017) doi:10.1038/s41598-017-01122-7
Miklós Erdélyi, József Sinkó, Tamás Gajdos and Tibor Novák – “Enhanced simulator software for image validation and interpretation for multimodal localization super-resolution fluorescence microscopy “, Proc. SPIE 10071, Single Molecule Spectroscopy and Superresolution Imaging X, 100710X (February 21, 2017); doi:10.1117/12.2250116;
A practical method has been presented for polarization sensitive localization based super-resolution microscopy using a birefringent dual wedge. The measurement of the polarization degree at single molecule level can reveal the chemical and physical properties of the local environment of the fluorescent dye molecule and can hence provide information about the sub-diffraction sized structure of biological samples. Polarization sensitive STORM imaging of the F-actins proved correlation between the orientation of fluorescent dipoles and the axis of the fibril.