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@inproceedings{Hladuvka-2024-DGMM,
title = {Fitting egg-shapes to discretized object boundaries},
author = {Jiří Hladůvka and Walter G. Kropatsch},
year = 2024,
booktitle = {Discrete Geometry and Mathematical Morphology},
_publisher = {Springer Nature Switzerland},
_address = {Cham},
pages = {107--119},
doi = {10.1007/978-3-031-57793-2_9},
isbn = {978-3-031-57793-2},
}

@mastersthesis{Wolf-2023-MSc,
title = {Self-Supervised Learning for Medical Hyperspectral Image Segmentation},
author = {Fabian Wolf},
year = 2023,
school = {Heidelberg University},
}

@misc{Pelletier-2023-EggDS,
title = {Eggshapes: {A} collection of egg-shaped objects and their boundaries},
author = {Vincent Pelletier and Jiří Hladůvka},
year = 2023,
month = dec,
publisher = {TU Wien},
doi = {10.48436/de66n-2pj41},
howpublished = {dataset},
}

@inproceedings{Banaeyan_ICPRAM_2024,
title = {Distance Transform in Images and Connected Plane Graphs},
author = {Banaeyan, Majid and Kropatsch, Walter G.},
year = 2023,
booktitle = {International Conference on Pattern Recognition Applications and Methods},
publisher = {Springer, Lecture Notes in Computer Science},
volume = 14547,
pages = {19--32},
doi = {10.1007/978-3-031-54726-3_2},
}

@inproceedings{Banaeyan_GbR_2023,
title = {Reducing the Computational Complexity of the Eccentricity Transform of a Tree},
author = {Banaeyan, Majid and Kropatsch, Walter G.},
year = 2023,
booktitle = {Proceedings of the 13th AIPR-TC15 International Workshop on Graph Based Representation},
publisher = {Springer, Lecture Notes in Computer Science},
volume = 14121,
pages = {160--171},
doi = {10.1007/978-3-031-42795-4_15},
}

@inproceedings{Banaeyan_ICPRAM_2023,
title = {Distance Transform in Parallel Logarithmic Complexity},
author = {Banaeyan, Majid and Kropatsch, Walter G.},
year = 2023,
booktitle = {Proceedings of the 12th International Conference on Pattern Recognition Applications and Methods - ICPRAM},
publisher = {SciTePress},
pages = {115--123},
doi = {10.5220/0011681500003411},
}

@article{Rancourt-2023-AoBplants,
title = {Analyzing anatomy over three dimensions unpacks the differences in mesophyll diffusive area between sun and shade Vitis vinifera leaves},
author = {Guillaume Théroux-Rancourt and José Carlos Herrera and Klara Voggeneder and Federica De Berardinis and Natascha Luijken and Laura Nocker and Tadeja Savi and Susanne Scheffknecht and Moritz Schneck and Danny Tholen},
year = 2023,
month = {01},
journal = {AoB Plants},
doi = {10.1093/aobpla/plad001},
issn = {2041-2851},
url = {https://doi.org/10.1093/aobpla/plad001},
note = {plad001},
eprint = {https://academic.oup.com/aobpla/advance-article-pdf/doi/10.1093/aobpla/plad001/48907756/plad001\_suppl\_supplementary\_material.pdf},
}

@inproceedings{2022-OAGM-Grexova,
title = {Towards Uncertainty Detection in Automated Leaf Tissue Segmentation},
author = {Ráchel Grexová and Klara Voggeneder and Danny Tholen and Guillaume Theroux-Rancourt and Walter Kropatsch and Jiří Hladůvka},
year = 2022,
booktitle = {OAGM Workshop: Digitalization for Smart Farming and Forestry},
editor = {Bűrstmayr, Hermann and Gronauer, Andreas and Holzinger, Andreas and Roth, Peter M. and Stampfer, Karl},
pages = {47--53},
doi = {10.3217/978-3-85125-954-4-07},
}

@article{trueba2022three,
title = {The three-dimensional construction of leaves is coordinated with water use efficiency in conifers},
author = {Trueba, Santiago and Th{\'e}roux-Rancourt, Guillaume and Earles, J Mason and Buckley, Thomas N and Love, David and Johnson, Daniel M and Brodersen, Craig},
year = 2022,
journal = {New Phytologist},
publisher = {Wiley Online Library},
volume = 233,
number = 2,
pages = {851--861},
doi = {10.1111/nph.17772},
}

@article{borsuk2022structural,
title = {Structural organization of the spongy mesophyll},
author = {Borsuk, Aleca M and Roddy, Adam B and Th{\'e}roux-Rancourt, Guillaume and Brodersen, Craig R},
year = 2022,
journal = {The New Phytologist},
publisher = {Wiley-Blackwell},
volume = 234,
number = 3,
pages = 946,
doi = {10.1111/nph.17971},
}

@thesis{Troger-2022-BSc,
title = {Semantic Segmentation of {3D} Volumetric Data using Point-Based Neural Networks},
author = {Oliver Troger},
year = 2022,
school = {Vienna University of Technology},
type = {Bachelor's Thesis},
}

@inproceedings{Banaeyan-2022-ICISPR,
title = {Removing Redundancies in Binary Images},
author = {Banaeyan, Majid and Batavia, Darshan and Kropatsch, Walter G.},
year = 2022,
booktitle = {International Conference on Intelligent Systems and Patterns Recognition},
pages = {221--233},
doi = {10.1007/978-3-031-08277-1_19},
place = {Hammamet, Tunisia, March 24-25, 2022},
}

@inproceedings{2022-OAGM-Banaeyan,
title = {Redundant 1-cells in Multi-labeled {2-Gmap} Irregular Pyramids},
author = {Majid Banaeyan and Walter G. Kropatsch and Jiří Hladůvka},
year = 2022,
booktitle = {OAGM Workshop: Digitalization for Smart Farming and Forestry},
pages = {5--11},
doi = {10.3217/978-3-85125-954-4-01},
}

@inproceedings{Banaeyan-2022-ICPRAI,
title = {Parallel {${\cal O}(\log(n))$} Computation of the Adjacency of Connected Components},
author = {Banaeyan, Majid and Kropatsch, Walter G.},
year = 2022,
booktitle = {International Conference on Pattern Recognition and Artificial Intelligence},
pages = {102--113},
doi = {10.1007/978-3-031-09282-4_9},
__place = {Paris, France, June 1-3, 2022},
}

@inproceedings{2022-OAGM-Sauzeau,
title = {Modeling the Diffusion of {CO$_2$} inside Leaves},
author = {Yannis Sauzeau and Walter Kropatsch and Jiří Hladůvka},
year = 2022,
booktitle = {OAGM Workshop: Digitalization for Smart Farming and Forestry},
pages = {70--72},
doi = {10.3217/978-3-85125-954-4-11},
}

@techreport{TR155,
title = {Learning-based Leaf Cell Instance Segmentation},
author = {Fabian Wolf},
year = 2022,
number = {PRIP-TR-155},
url = {https://www.prip.tuwien.ac.at/pripfiles/trs/tr155.pdf},
institution = {PRIP, TU Wien},
abstract = {Due to climate change, variability of temperature and rainfall increases. Based on this, understanding changes in leaf anatomy and function under those conditions is desirable. We aim to advance the understanding of changes in leaf anatomy by investigating deep- learning based instance segmentation of leaf cells. Accordingly, state-of-the-art (cell) in- stance segmentation methods are discussed. Based on the discussion, we investigated 2D- and 3D-Cellpose with and without additional semantic information. In general, we found that Cellpose is not suited well for the task, but might be suited for segmenting roundish (sponge and palisade) cells. We conclude that further research is required and propose to investigate embedding-based approaches.},
}

@techreport{TR154,
title = {Implicit unbounded n-{G}maps for images: A membrane-centric encoding using bit-flips},
author = {Jiří Hladůvka and Florian Bogner and Walter G. Kropatsch},
year = 2022,
number = {PRIP-TR-154},
url = {https://www.prip.tuwien.ac.at/pripfiles/trs/tr154.pdf},
institution = {PRIP, TU Wien},
abstract = {The practical use of generalized combinatorial maps(n-Gmaps) to represent nD-images is limited by large memory requirements. Implicit representations, if well designed, can come to the rescue. Unbounded n-Gmaps are surrounded by an infinite background region that renders pixel-oriented implicit representation schemes inconvenient. The contribution of this paper is twofold. First, we propose an implicit, membrane-centric (rather than pixel-centric) arrangement of darts in unbounded n-Gmaps. Second, we introduce involutions based on bit flips, which allow efficient iterations in membranes and have the potential to speed up computations. We have validated our approach on a variety of 2D and 3D images, including those whose memory requirements would far exceed the main memory.},
}

@inproceedings{Bogner-2022-DGMM,
title = {Implicit Encoding and Simplification/Reduction of {nGmaps}},
author = {Florian Bogner and Jiří Hladůvka and Walter G. Kropatsch},
year = 2022,
booktitle = {Discrete Geometry and Mathematical Morphology},
publisher = {Springer International Publishing},
pages = {110--122},
doi = {10.1007/978-3-031-19897-7_10},
isbn = {978-3-031-19897-7},
editor = {Baudrier, {\'E}tienne and Naegel, Beno{\^i}t and Kr{\"a}henb{\"u}hl, Adrien and Tajine, Mohamed},
_address = {Cham},
abstract = {This paper aims to present a new method of translating labeled 3D scans of biological tissues into Generalized Maps (nGmaps). Creating such nGmaps from labeled images is a solved problem in 2D and 3D using incremental algorithms. We present a new approach that works in arbitrary dimensions. To achieve this in an effective manner, we perform the necessary operations implicitly using theory rather than explicitly in memory. First we define implicit nGmaps. We then present a scheme to construct said nGmap representing an nD pixel/voxel-grid implicitly. Thirdly we give a description of the process needed to reduce such implicit nGmap. We demonstrate that our implicit approach is able to reduce nGmaps in a fraction of otherwise necessary memory.},
}

@article{Banaeyan-2022-JENRS,
title = {Fast Labeled Spanning Tree in Binary Irregular Graph Pyramids},
author = {Majid Banaeyan and Walter G. Kropatsch},
year = 2022,
journal = {Journal of Engineering Research and Sciences},
volume = 1,
number = 10,
pages = {69--78},
doi = {10.55708/js0110009},
_keywords = {irregular pyramid,parallel processing,spanning tree,total order},
file = {:D\:/JENRS/Publication/JENRS_0110009.pdf:pdf},
keywords = {irregular pyramid,parallel processing,spanning tree,total order},
}

@inproceedings{Banaeyan-2022-SSPR,
title = {Fast Distance Transforms in Graphs and in {G}maps},
author = {Banaeyan, Majid and Carratù, Carmine and Kropatsch, Walter G. and Jiří Hladůvka},
year = 2022,
booktitle = {IAPR Joint International Workshops on Statistical Techniques in Pattern Recognition (SPR 2022) and Structural and Syntactic Pattern Recognition (SSPR 2022)},
pages = {193--202},
doi = {10.1007/978-3-031-23028-8_20},
url = {https://doi.org/10.1007/978-3-031-23028-8_20},
__place = {{M}ontreal, {C}anada},
}

@techreport{TR152,
title = {Efficient contraction kernel selection with a knight's move},
author = {Luca Boccia},
year = 2022,
number = {PRIP-TR-152},
url = {https://www.prip.tuwien.ac.at/pripfiles/trs/tr152.pdf},
institution = {PRIP, TU Wien},
abstract = {Irregular image pyramids built with combinatorial map representations of graphs (Combinatorial Pyramids) enable the usage of topological information for both down-sampling and up-sampling, used for compactness and for surface reconstruction respectively. The hierarchy and the complexity of the image pyramid are mainly controlled by the choice of a contraction kernel. In this work we propose a formal grammar for selecting contraction kernels for plateau regions in binary and multi-label images. Our method enables parallel computing through selection of independent edges to contract, and efficiency is achieved by finding a good balance between the number of contraction and simplification operations, needed after the application of the kernel. We show that our method achieves regularity and produces pyramids of height similar to regular pyramid schemes on plateau regions. Finally, we present possible solutions to generalize our approach to design a Connected Component Labeling algorithm that is both efficient and correct.},
}

@techreport{TR153,
title = {Distance transforms on {G}maps},
author = {Carmine Carratù},
year = 2022,
number = {PRIP-TR-153},
url = {https://www.prip.tuwien.ac.at/pripfiles/trs/tr153.pdf},
institution = {PRIP, TU Wien},
abstract = {The distance transform computes for every pixel of a binary image the distance from the closest pixel in the background. The operator can be generalized to work with other data structures like graphs or combinatorial maps. In this work we describe how to compute the distance transform of a generalized map, and we propose two algorithms to compute re- spectively the distance transform of unweighted and weighted generalized maps. Moreover, we describe how such algorithms can be used for the ”Water’s gateway to heaven” project to compute the diffusion distance and Voronoi diagrams that can be used to study the gas exchange process that occurs in plant leaves.},
}

@inproceedings{2022-OAGM-Palmrich,
title = {An unsupervised, shape-based {3D} cell instance segmentation method for plant tissues},
author = {Alexander Palmrich and Klara Voggeneder and Danny Tholen and Guillaume Theroux-Rancourt and Jiří Hladůvka and Walter Kropatsch},
year = 2022,
booktitle = {OAGM Workshop: Digitalization for Smart Farming and Forestry},
pages = {54--59},
doi = {10.3217/978-3-85125-954-4-08},
}

@thesis{Grexova-2022-BSc,
title = {{U-Net} Segmentation of the Poplar Leaf Using Orthogonal Axes Ensemble},
author = {Ráchel Grexová},
year = 2022,
school = {Vienna University of Technology},
type = {Bachelor's Thesis},
}

@thesis{Tulacs-2023-BSc,
title = {Supporting image annotation by building morphological pyramids},
author = {Janika Tulacs},
year = 2023,
school = {Vienna University of Technology},
type = {Bachelor's Thesis},
}



@article{Harwood-2021-Plant,
title = {Understanding airspace in leaves: {3D} anatomy and directional tortuosity},
author = {Richard Harwood and Guillaume Théroux-Rancourt and Margaret M Barbour},
year = 2021,
journal = {Plant, Cell \& Environment},
volume = 44,
number = 8,
pages = {2455--2465},
doi = {10.1111/pce.14079},
}

@inproceedings{Bogner2020,
title = {Border Propagation: A Novel Approach to Determine Slope Region Decompositions},
author = {Bogner, Florian and Palmrich, Alexander and Kropatsch, Walter G.},
year = 2020,
booktitle = {Proceedings of the Joint Austrian Computer Vision and Robotics Workshop},
publisher = {Technische Universität Graz},
pages = {137--142},
doi = {10.3217/978-3-85125-752-6-31},
url = {http://www.prip.tuwien.ac.at/people/krw/more/papers/2020/OeAGM/Bogner2020.pdf},
note = {Isbn 978-3-85125-752-6},
editor = {Roth, Peter M. and Steinbauer, Gerald and Fraundorfer, Friedrich and Brandstötter, Mathias and Perko, Roland},
}

@article{Hladuvka-2024-JMIV,
title = {Enhanced iterative egg-shape fitting to discretized object boundaries},
author = {Jiří Hladůvka and Walter G. Kropatsch},
year = {to appear},
journal = {Journal of Mathematical Imaging and Vision},
}

@phdthesis{Banaeyan-2024-PhD,
title = {Redundant Edges and Parallel Algorithms in Binary Irregular Graph Pyramids},
author = {Majid Banaeyan},
year = 2024,
doi = {10.34726/hss.2024.103865},
school = {Vienna University of Technology},
}

@article{tholen_gasanalyzer_2024,
title = {{GasanalyzeR}: {Advancing} {Reproducible} {Research} using a {New} {R} {Package} for {Photosynthesis} {Data} {Workflows}},
shorttitle = {{GasanalyzeR}},
author = {Tholen, Danny},
year = 2024,
month = jun,
journal = {AoB Plants},
volume = 16,
number = 4,
pages = {plae035},
doi = {10.1093/aobpla/plae035},
issn = {2041-2851},
url = {https://doi.org/10.1093/aobpla/plae035},
urldate = {2024-07-16}
}

@inproceedings{tholen_leaf_2022,
title = {Leaf {Structure} and {Function} in {Four} {Dimensions}: {Non}-invasive {MicroCT} {Imaging} {During} {Gas}-exchange {Measurements}},
author = {Tholen, Danny and Scheffknecht, Susanne and Voggeneder, Klara and Weiss, Elisabeth and Théroux-Rancourt, Guillaume},
year = 2022,
booktitle = {{EGU} {General} {Assembly} {Conference} {Abstracts}},
pages = {EGU22--9801}
}

@article{theroux-rancourt_maximum_2021,
title = {Maximum {CO$_2$} diffusion inside leaves is limited by the scaling of cell size and genome size},
author = {Théroux-Rancourt, Guillaume and Roddy, Adam B. and Earles, J. Mason and Gilbert, Matthew E. and Zwieniecki, Maciej A. and Boyce, C. Kevin and Tholen, Danny and McElrone, Andrew J. and Simonin, Kevin A. and Brodersen, Craig R.},
year = 2021,
month = feb,
journal = {Proceedings. Biological Sciences},
volume = 288,
number = 1945,
pages = 20203145,
doi = {10.1098/rspb.2020.3145},
issn = {1471-2954},
language = {eng},
pmid = 33622134,
pmcid = {PMC7934972},
keywords = {Photosynthesis, Carbon Dioxide, Mesophyll Cells, Plant Leaves, gas diffusion, Cell Size, Genome Size, intercellular airspace, leaf mesophyll, vascular plants}
}

@mastersthesis{Koller-2022-MSc,
title = {Phenotyping for drought stress tolerance with a focus on leaf anatomy and physiology},
author = {Lukas Michael Koller},
year = 2022,
doi = {10.25365/thesis.70965},
school = {University Vienna},
}

@article{Zekri-2024-Freeze,
title = {A rapid freezing method to determine tissue layer thickness in drought-stressed leaves},
author = {Zekri, Maryam Alsadat and Leimhofer, Carina and Drexler, Nicole and Lang, Ingeborg},
year = 2024,
journal = {Journal of Microscopy},
pages = {1--9},
doi = {10.1111/jmi.13272},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jmi.13272},
keywords = {Arabidopsis thaliana, drought stress, genotypes, mesophyll, plunge freezing, SEM},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/jmi.13272},
}

@manual{TholenRpackage,
title = {gasanalyzer: Import, Recompute and Analyze Data from Portable Gas Analyzers},
author = {Danny Tholen},
year = 2024,
url = {https://CRAN.R-project.org/package=gasanalyzer},
note = {{R} package version 0.4.1},
}
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