TY - CONF A1 - Rühle, Bastian A1 - Hodoroaba, Vasile-Dan T1 - Automatic Image Segmentation and Analysis using Neural Networks N2 - We present a workflow for obtaining fully trained artificial neural networks that can perform automatic particle segmentations of agglomerated, non-spherical nanoparticles from electron microscopy images “from scratch”, without the need for large training data sets of manually annotated images. This is achieved by using unsupervised learning for most of the training dataset generation, making heavy use of generative adversarial networks and especially unpaired image-to-image translation via cycle-consistent adversarial networks. The whole process only requires about 15 minutes of hands-on time by a user and can typically be finished within less than 12 hours when training on a single graphics card (GPU). After training, SEM image analysis can be carried out by the artificial neural network within seconds, and the segmented images can be used for automatically extracting and calculating various other particle size and shape descriptors. T2 - Machine Learning Workshop CY - Online Meeting DA - 18.03.2021 KW - Electron Microscopy KW - Neural Networks KW - Artificial Intelligence KW - Image Segmentation KW - Automated Image Analysis PY - 2021 AN - OPUS4-52304 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Daly, H.C A1 - Matikonda, S.S A1 - Steffens, H.C A1 - Rühle, Bastian A1 - Resch-Genger, Ute A1 - Ivanic, J. A1 - Schermann, M.J T1 - Daly_Photochem Photobiol 2021_Ketone Incorporation Extends the Emission Properties of the Xanthene Scaffold JF - Photochemistry and Photobiology N2 - Imaging in the shortwave-infrared region (SWIR, λ = 1000–2500 nm) has the potential to enable deep tissue imaging with high resolution. Critical to the development of these Methods is the identification of low molecular weight, biologically compatible fluorescent probes that emit beyond 1000 nm. Exchanging the bridging oxygen atom on the xanthene scaffold (C10’ position) with electron withdrawing groups has been shown to lead to significant redshifts in absorbance and emission. Guided by quantum chemistry computational modeling studies, we investigated the installation of a Ketone bridge at the C10’ position. This simple modification extends the absorbance maxima to 860 nm and the emission beyond 1000 nm, albeit with reduced photon output. Overall, These studies demonstrate that broadly applied xanthene dyes can be extended into the SWIR range. KW - Flourescence KW - Optical probe KW - Dye KW - Photophysics KW - Quantum yield KW - Mechanism KW - NIR KW - SWIR KW - Imaging KW - Reliability KW - Method KW - Quality assurance PY - 2021 DO - https://doi.org/10.1111/php.13544 SN - 1751-1097 VL - 98 IS - 2 SP - 325 EP - 333 PB - Wiley Online Library AN - OPUS4-54080 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Rühle, Bastian A1 - Krumrey, Julian Frederic A1 - Hodoroaba, Vasile-Dan T1 - Dataset accompanying the publication "Workflow towards automated segmentation of agglomerated, non-spherical particles from electron microscopy images using artificial neural networks" N2 - This dataset accompanies the following publication, first published in Scientific Reports (www.nature.com/articles/s41598-021-84287-6): B. Ruehle, J. Krumrey, V.-D. Hodoroaba, Scientific Reports, Workflow towards Automated Segmentation of Agglomerated, Non-Spherical Particles from Electron Microscopy Images using Artificial Neural Networks, DOI: 10.1038/s41598-021-84287-6 It contains electron microscopy micrographs of TiO2 particles, the corresponding segmentation masks, and their classifications into different categories depending on their visibility/occlusion. Please refer to the publication and its supporting information for more details on the acquisition and contents of the dataset, as well as the GitHub repository at https://github.com/BAMresearch/automatic-sem-image-segmentation KW - Electron microscopy KW - Neural networks KW - Image segmentation KW - Automated image analysis PY - 2021 DO - https://doi.org/10.5281/zenodo.4563942 PB - Zenodo CY - Geneva AN - OPUS4-52246 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Kunc, F. A1 - Nirmalananthan-Budau, Nithiya A1 - Rühle, Bastian A1 - Sung, Y. A1 - Johnston, L.J. A1 - Resch-Genger, Ute T1 - Interlaboratory Comparison on the Quantification of Total and Accessible Amine Groups on Silica Nanoparticles with qNMR and Optical Assays JF - Analytical chemistry N2 - Risk assessment of nanomaterials requires not only standardized toxicity studies but also validated methods for nanomaterial surface characterization with known uncertainties. In this context, a first bilateral interlaboratory comparison on Surface group quantification of nanomaterials is presented that assesses different reporter-free and labeling methods for the quantification of the total and accessible number of amine functionalities on commercially available silica nanoparticles that are widely used in the life sciences. The overall goal of this comparison is the identification of optimum methods as well as achievable measurement uncertainties and the comparability of the results across laboratories. We also examined the robustness and ease of implementation of the applied analytical methods and discussed method-inherent limitations. In summary, this comparison presents a first step toward the eventually required standardization of methods for surface group quantification. KW - Nano KW - Nanomaterial KW - Surface KW - Method KW - QNMR KW - Quantification KW - Comparison KW - Quality assurance KW - Optical probe KW - Sensor KW - Interlabority comparison KW - Standardization KW - Optical assay KW - Functional group analysis KW - Silica KW - Particle KW - Safety KW - Environment PY - 2021 DO - https://doi.org/10.1021/acs.analchem.1c02162 SN - 1520-6882 VL - 93 IS - 46 SP - 15271 EP - 15278 PB - ASC Publications AN - OPUS4-53818 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Rühle, Bastian A1 - Krumrey, Julian Frederic A1 - Hodoroaba, Vasile-Dan T1 - Workflow towards automated segmentation of agglomerated, non‑spherical particles from electron microscopy images using artificial neural networks JF - Scientific reports N2 - We present a workflow for obtaining fully trained artificial neural networks that can perform automatic particle segmentations of agglomerated, non-spherical nanoparticles from scanning electron microscopy images “from scratch”, without the need for large training data sets of manually annotated images. The whole process only requires about 15 minutes of hands-on time by a user and can typically be finished within less than 12 hours when training on a single graphics card (GPU). After training, SEM image analysis can be carried out by the artificial neural network within seconds. This is achieved by using unsupervised learning for most of the training dataset generation, making heavy use of generative adversarial networks and especially unpaired image-to-image translation via cycle-consistent adversarial networks. We compare the segmentation masks obtained with our suggested workflow qualitatively and quantitatively to state-of-the-art methods using various metrics. Finally, we used the segmentation masks for automatically extracting particle size distributions from the SEM images of TiO2 particles, which were in excellent agreement with particle size distributions obtained manually but could be obtained in a fraction of the time. KW - Electron microscopy KW - Neural networks KW - Artificial intelligence KW - Image segmentation KW - Automated image analysis PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-522454 DO - https://doi.org/10.1038/s41598-021-84287-6 VL - 11 IS - 1 SP - 4942 PB - Springer Nature AN - OPUS4-52245 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -