In this repository you find the code used to register, evaluate and analyse the data in our publication. Please cite our publication when using our code:
Kylies, D., Zimmermann, M., Haas, F., Schwerk, M., Kuehl, M., Brehler, M., Czogalla, J., Hernandez, L. C., Konczalla, L., Okabayashi, Y., Menzel, J., Edenhofer, I., Mezher, S., Aypek, H., Dumoulin, B., Wu, H., Hofmann, S., Kretz, O., Wanner, N., Tomas, N. M., Krasemann, S., Glatzel, M., Kuppe, C., Kramann, R., Banjanin, B., Schneider, R. K., Urbschat, C., Arck, P., Gagliani, N., van Zandvoort, M., Wiech, T., Grahammer, F., Sáez, P. J., Wong, M. N., Bonn, S., Huber, T. B., Puelles, V. G. (2023). Expansion-enhanced super-resolution radial fluctuations enable nanoscale molecular profiling of pathology specimens. Nature Nanotechnology. doi:10.1038/s41565-023-01328-z.
Script that registers the time stacks saved as tiff files in a folder and calculated the SSIM and MSE to evaluate the registrations.
Notebook that was used to compare the SSIM between ridges and original images for ExM, ExSRRF and STED images.
Notebook to extract regions of interest and ridges (slit diaphragm) and calculate their densities
Notebook to extract regions of interest and ridges (ER) and calculate their densities
Notebook to compute the local spacing of ridge images. Local spacing calculation is based on the local_thickness plugin of Fiji (ImageJ) and was ported to python and adapted for our 2D use case.
Output of local_spacing.ipynb for given sythetic test image:
- original
- distance transformed image
- ridge image
- local spacing image
