@article{19003,
  abstract     = {Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that expansion microscopy can be applied to increase effective imaging resolution in Arabidopsis root specimens. },
  author       = {Gallei, Michelle C and Truckenbrodt, Sven M and Kreuzinger, Caroline and Inumella, Syamala and Vistunou, Vitali and Sommer, Christoph M and Tavakoli, Mojtaba and Agudelo Duenas, Nathalie and Vorlaufer, Jakob and Jahr, Wiebke and Randuch, Marek and Johnson, Alexander J and Benková, Eva and Friml, Jiří and Danzl, Johann G},
  issn         = {1532-298X},
  journal      = {The Plant Cell},
  number       = {4},
  publisher    = {Oxford University Press},
  title        = {{Super-resolution expansion microscopy in plant roots}},
  doi          = {10.1093/plcell/koaf006},
  volume       = {37},
  year         = {2025},
}

@phdthesis{19722,
  author       = {Inumella, Syamala},
  isbn         = {978-3-99078-059-6},
  issn         = {2663-337X},
  pages        = {113},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Molecular mechanisms of microtubule reorganization in elongating root epidermal cells}},
  doi          = {10.15479/AT-ISTA-19722},
  year         = {2025},
}

@unpublished{18689,
  abstract     = {Multiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A tranfer learning framework is further devised to allow our AutoUnmix adapting to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool to study the interaction process of different organelles labeled by multiple fluorophores.},
  author       = {Gallei, Michelle C and Truckenbrodt, Sven M and Kreuzinger, Caroline and Inumella, Syamala and Vistunou, Vitali and Sommer, Christoph M and Tavakoli, Mojtaba and Agudelo Duenas, Nathalie and Vorlaufer, Jakob and Jahr, Wiebke and Randuch, Marek and Johnson, Alexander J and Benková, Eva and Friml, Jiří and Danzl, Johann G},
  booktitle    = {bioRxiv},
  title        = {{Super-resolution expansion microscopy in plant roots}},
  doi          = {10.1101/2024.02.21.581330},
  year         = {2024},
}