@inproceedings{WesterhoffMayeBrandtetal.2002, author = {Westerhoff, Malte and Maye, Alexander and Brandt, Robert and Menzel, Randolf}, title = {3D Geometry Reconstruction in Neuroanatomy}, booktitle = {International Neuroscience Summit Abstract Book}, address = {Berlin, Germany}, pages = {49}, year = {2002}, language = {en} } @inproceedings{BrandtMalunSteegeetal.1999, author = {Brandt, Robert and Malun, Dagmar and Steege, A. and Z{\"o}ckler, Malte and Menzel, Randolf}, title = {Three Dimensional Reconstruction of Honey Bee Mushroom Bodies}, booktitle = {Annual Meeting of the Society for Neuroscience, Abstr. 25}, pages = {861}, year = {1999}, language = {en} } @inproceedings{RybakKussHolleretal.2009, author = {Rybak, J{\"u}rgen and Kuß, Anja and Holler, Wolfgang and Brandt, Robert and Hege, Hans-Christian and Menzel, Randolf}, title = {The HoneyBee Standard Brain (HSB) - a versatile atlas tool for integrating data and data exchange in the neuroscience community}, volume = {10 (Suppl 1):P1}, booktitle = {BMC Neuroscience}, doi = {10.1186/1471-2202-10-S1-P1}, year = {2009}, language = {en} } @article{BrandtRohlfingRybaketal.2005, author = {Brandt, Robert and Rohlfing, Torsten and Rybak, J{\"u}rgen and Krofczik, Sabine and Maye, Alexander and Westerhoff, Malte and Hege, Hans-Christian and Menzel, Randolf}, title = {A three-dimensional average-shape atlas of the honeybee brain and its applications}, volume = {492(1)}, journal = {Journal of Comparative Neurology}, pages = {1 -- 19}, year = {2005}, language = {en} } @misc{ZoecklerReinBrandtetal.2001, author = {Z{\"o}ckler, Malte and Rein, Karlheinz and Brandt, Robert and Stalling, Detlev and Hege, Hans-Christian}, title = {Creating Virtual Insect Brains with Amira}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-6589}, number = {01-32}, year = {2001}, abstract = {By combining techniques of preparation, histology, confocal microscopy, data visualization and data processing, we have created and recently published a standard brain model for drosophila and honey bee brains. This report describes the algorithms and implementation of the corresponding software modules. At the same time it serves as a user's guide for scientist who want to reproduce the results for differerent species or mutants.}, language = {en} } @article{HajarolasvadiSunkaraKhavnekaretal.2022, author = {Hajarolasvadi, Noushin and Sunkara, Vikram and Khavnekar, Sagar and Beck, Florian and Brandt, Robert and Baum, Daniel}, title = {Volumetric macromolecule identification in cryo-electron tomograms using capsule networks}, volume = {23}, journal = {BMC Bioinformatics}, number = {360}, doi = {10.1186/s12859-022-04901-w}, year = {2022}, abstract = {Background: Despite recent advances in cellular cryo-electron tomography (CET), developing automated tools for macromolecule identification in submolecular resolution remains challenging due to the lack of annotated data and high structural complexities. To date, the extent of the deep learning methods constructed for this problem is limited to conventional Convolutional Neural Networks (CNNs). Identifying macromolecules of different types and sizes is a tedious and time-consuming task. In this paper, we employ a capsule-based architecture to automate the task of macro- molecule identification, that we refer to as 3D-UCaps. In particular, the architecture is composed of three components: feature extractor, capsule encoder, and CNN decoder. The feature extractor converts voxel intensities of input sub-tomograms to activities of local features. The encoder is a 3D Capsule Network (CapsNet) that takes local features to generate a low-dimensional representation of the input. Then, a 3D CNN decoder reconstructs the sub-tomograms from the given representation by upsampling. Results: We performed binary and multi-class localization and identification tasks on synthetic and experimental data. We observed that the 3D-UNet and the 3D-UCaps had an F1-score mostly above 60\% and 70\%, respectively, on the test data. In both network architectures, we observed degradation of at least 40\% in the F1-score when identifying very small particles (PDB entry 3GL1) compared to a large particle (PDB entry 4D8Q). In the multi-class identification task of experimental data, 3D-UCaps had an F1-score of 91\% on the test data in contrast to 64\% of the 3D-UNet. The better F1-score of 3D-UCaps compared to 3D-UNet is obtained by a higher precision score. We speculate this to be due to the capsule network employed in the encoder. To study the effect of the CapsNet-based encoder architecture further, we performed an ablation study and perceived that the F1-score is boosted as network depth is increased which is in contrast to the previously reported results for the 3D-UNet. To present a reproducible work, source code, trained models, data as well as visualization results are made publicly available. Conclusion: Quantitative and qualitative results show that 3D-UCaps successfully perform various downstream tasks including identification and localization of macro- molecules and can at least compete with CNN architectures for this task. Given that the capsule layers extract both the existence probability and the orientation of the molecules, this architecture has the potential to lead to representations of the data that are better interpretable than those of 3D-UNet.}, language = {en} }