Peter Pietrzyk, Neen Phan-Udom, Chartinun Chutoe, Lise Pingault, Ankita Roy, Marc Libault, Patompong Johns Saengwilai, Alexander Bucksch. DIRT/μ – Automated extraction of root hair traits using combinatorial optimization. bioRxiv 2024.01.18.576310; doi: https://doi.org/10.1101/2024.01.18.576310
2023: Swetnam, T.L., Antin, P.B., Bartelme, R., Bucksch, A., Camhy, D., Chism, G., Choi, I., Cooksey, A. M., Cosi, M., Cowen, C., Culshaw-Maurer, M., Davey, R., Davey, S., Devisetty, U., Edgin, T., Edmonds, A., Fedorov, D., Frady, J., Fonner, J., Gillan, J.K., Hossain, I., Joyce, B., Lang, K., Lee, T., Littin, S., Mcewen, I., Merchant, N., Micklos, D., Nelson, A., Ramsey, A., Roberts, S., Sarando, P., Skidmore, E., Song, J., Sprinkle, M.M., Srinivasan, S., Strootman, J.D., Stryeck, S., Tuteja, R., Vaughn, M., Wali, M., Wall, M., Walls, R., Wang, L., Wickizer, T., Williams, J., Wregglesworth, J., Lyons, E.: CyVerse: Cyberinfrastructure for Open Science. PLoS Computational Biology 20(2) e101270.
2022: Kawa, D., Thiombiano, B., Shimels, M., Taylor, T., Walmsley, A., Vahldick, H. E., Leite, M.F.A., Musa, Z., Bucksch, A., Dini-Andreote, F., Chen, A.J., Daksa, J., Etalo, D., Tessema, T., Kuramae, E.E., Raaijmakers, J.M., Bouwmeester, H., Brady, S.M.: The soil microbiome reduces Striga infection of sorghum by modulation of host-derived signaling molecules and root development. Cell Reports 43(4).
2022: Temme, A.A., Kerr, K.L., Nolting, K.M., Dittmar, E.L., Masalia, R.R., Bucksch, A.K., Burke, J.M., Donovan, L.A.: Exceeding expectations: the genomic basis of nitrogen utilization efficiency and integrated trait plasticity as avenues to improve nutrient stress tolerance in cultivated sunflower (Helianthus annuus L.). Journal of Experimental Botany, erae025.
2023: Swartz, L.G., Liu, S., Dahlquist, D., Kramer, S.T., Walter, E.S., McInturf, S.A., Bucksch, A., Mendoza-Cozatl, D.G.: OPEN leaf: an open-source cloud-based phenotyping system for tracking dynamic changes at leaf-specific resolution in Arabidopsis. The Plant Journal 1095(2).
2023: LeBauer, D., Bucksch, A., Clarke, J., Potts, J., Roy, S.: Increasing racial diversity in the North American Plant Phenotyping Network through conference participation support. The Plant Phenome Journal 6(1), pp. e20075.
2023 Liu, S., Bonelli, W.P., Pietrzyk, P., Bucksch, A.: Comparison of open-source three-dimensional reconstruction pipelines for maize-root phenotyping. The Plant Phenome Journal 6(1), pp. e20068.
2023: Knapp-Wilson, J., Bohn Reckziegel, R., Thapa Magar, S., Bucksch, A., Chavez, D. J.: Three-dimensional phenotyping of peach tree-crown architecture utilizing terrestrial laser scanning. The Plant Phenome Journal6(1), pp. e20073.
2022: H.M. Schneider, V.S.N. Lor, M.T. Hanlon, A. Perkins, S.M. Kaeppler, A.N. Borkar, R. Bhosale, X. Zhang, J. Rodriguez, A. Bucksch, M.J. Bennett, K.M. Brown, J.P. Lynch: Root angle in maize influences nitrogen capture and is regulated by CBL‐interacting serine/threonine‐protein kinase 15 (ZmCIPK15). Plant, Cell & Enviroment 45(3), pp. 837-853
2021: A. Roy, A. Bucksch: Root Hairs vs. Trichomes: Not everyone is straight! Current Opinion in Plant Biology 64, 102151.
2021: S. Liu, C.S. Barrow, M. Hanlon, J.P. Lynch, A. Bucksch: DIRT/3D: 3D root phenotyping for field grown maize (Zea mays). Plant Physiology 187(2), pp. 739–757.
2021: D. Kawa, T. Taylor, B. Thiombiano, Z. Musa, H.E. Vahldick, A. Walmsley, A. Bucksch, H. Bouwmeester, S.M. Brady: Characterization of growth and development of sorghum genotypes with differential susceptibility to Striga hermonthica, Journal of Experimental Botany 72(22), pp. 7970–7983.
2021: R. Dale, S. Oswald, A. Jalihal, M.-F.Laporte, D.M. Fletcher, A. Hubbard, S.-H. Shiu, A.D.L. Nelson, A. Bucksch: Overcoming the challenges to enhancing experimental plant biology with computational modeling. Frontiers in Plant Science 12, 1266.
2020: J. Salungyu, S. Thaitad, A. Bucksch, J. Kengkanna, P.J. Saengwilai: From lab to field: Open tools facilitating the translation of maize root traits. Field Crops Research 255, 107872.
2020: M. Herrero-Huerta, A. Bucksch, E Puttonen, K.M. Rainey: Canopy Roughness: A New Phenotypic Trait to Estimate Aboveground Biomass from Unmanned Aerial System, Plant Phenomics, 6735967.
2020: Image-based root phenotyping links root architecture to micronutrient concentration in cassava. Plants, People, Planet 2(6), pp. 678-687.
2019: Architectural and anatomical responses of maize roots to agronomic practices in a semi‐arid environment
Zhan, A., Liu, J., Yue, S., Chen, X., Li, S., Bucksch, A.
Journal of Plant Nutrition and Soil Science. 182(5), pp. 751-762
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2019: Phenotypic variation of cassava root traits and their responses to drought
Kengkanna, J., Jakaew, P., Amawan, S., Busener, N., Bucksch, A., & Saengwilai, P.
Applications in plant sciences, 7(4), e01238.
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2018: Optical approaches to capture plant dynamics in time, space, and across scales
E. Puttonen, A. Bucksch, A. Zlinszky, N. Pfeifer
Frontiers in Plant Science 9
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2018: Comparing phenotypic variation of root traits in Thai rice (Oryza sativa L.) across growing systems
P. Saengwilai, S. Klinsawang, M. Sangachart, A. Bucksch
Applied Ecology and Environmental Research 16(2), pp. 1069-1083
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2017: The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology
J. Friesner, S. Assmann, R. Bastow, J. Bailey-Serres, J. Beynon, V. Brendel, C.R. Buell, A. Bucksch, W. Busch, T. Demura, J. Dinneny, C. Doherty, A. Eveland, P. Falter-Braun, M. Gehan, M. Gonzales, E. Grotewold, R. Gutiérrez, U. Kraemer, G. Krouk, S. Ma, R.J. Markelz, M. Megraw, B. Meyers, J. Murray, N. Provart, S. Rhee, R. Smith, E. Spalding, C. Taylor, T. Teal, K. Torii, C. Town, M. Vaughn, R. Vierstra, D. Ware, O. Wilkins, C. Williams, S. Brady
Plant Physiology 175(4), pp. 1499-1509
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2017: Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences
A. Bucksch, A. Atta-Boateng , A.F. Azihou , D. Battogtokh, A. Baumgartner, B.M. Binder, S. A. Braybrook , C. Chang, V. Coneva, T.J. DeWitt, A.G. Fletcher, M. A. Gehan, D. H. Diaz-Martinez, L. Hong, A. S. Iyer-Pascuzzi, L. L. Klein Laura, S. Leiboff, M. Li, J. P. Lynch, A. Maizel, J. N. Maloof, R. J. C. Markelz, C. C. Martinez, L. A. Miller, W. Mio, W. Palubicki, H. Poorter, C. Pradal, C. A. Price, E. Puttonen, J. B. Reese, R. Rellán-Álvarez, E. P. Spalding, E. E. Sparks, C. N. Topp, J. H. Williams, D. H. Chitwood
Frontiers in Plant Science 8
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2017: Reshaping Plant Biology: Qualitative and Quantitative Descriptors for Plant Morphology
M. A. F. Balduzzi, B. M. Binder, A. Bucksch, C. Chang, L. Hong, A. S. Iyer-Pascuzzi, C. Pradal, E. E. Sparks
Frontiers in Plant Science 8
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2016: Overcoming the Law of the Hidden.
A. Bucksch, A. Das, H. Schneider, N. Merchant, J. S. Weitz
Trends in Plant Science 22(2), pp. 117-123
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2016: Genome-Wide Association Mapping and Agronomic Impact of Cowpea Root Architecture.
J. Burridge, H. Schneider, B.L. Huynh, P.A. Roberts, A. Bucksch, J. P. Lynch
Theoretical and Applied Genetics 130(2), pp. 419-431
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2016: Legume shovelomics: high-throughput phenotyping of common bean (Phaseolus vulgaris L.) and cowpea (Vigna unguiculata susp, unguilata) root architecture in the field.
J. Burridge, C. Jochua, A. Bucksch, J. P. Lynch
Field Crops Research 192, pp. 21-32
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2015: Digital Imaging of Root Traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics
A. Das, H. Schneider, J. Burridge, A. K. Martinez Ascanio, T. Wojciechowski, C. N. Topp, J. P. Lynch, J. S. Weitz, A. Bucksch (corresponding author)
Plant Methods 11(51)
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2014: Image-based high-throughput field phenotyping of crop roots.
A. Bucksch, J. Burridge, L. M. York, A. Das, E. Nord, J. S. Weitz, J. P. Lynch
Plant Physiology 166(2), pp. 470-486
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2014: A practical introduction to skeletons for the plant sciences.
A. Bucksch
Applications in Plant Sciences 2(8)
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2014: ClearedLeavesDB: an online database of cleared plant leaf image.
A. Das, A. Bucksch, C.A. Price, J.S. Weitz
Plant Methods 10(8)
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2014: The Fiber Walk: A Model of Tip-Driven Growth with Lateral Expansion.
A. Bucksch, G. Turk, J.S.Weitz
PLoS One 9(1), e85585
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2014: Breast height diameter estimation in high density airborne LiDAR data.
A. Bucksch, R. Lindenbergh, M.Z.A. Rahman, M.Menenti,
IEEE Geoscience and Remote Sensing Letters 11(6), pp. 156-1060
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2013: 3-dimensional phenotyping and quantitative trait locus mapping identifies core regions of the rice genome controlling root architecture
Topp, CN, AS Iyer-Pascuzzi, JT Anderson, C-R Lee, PR Zurek, O Symonova, Y Zheng, A Bucksch, Y Milyeko, T Galkovskyi, BT Moore, J Harer, H Edelsbrunner, T Mitchell-Olds, JS Weitz, PN Benfey,
PNAS 110(18), E1695-E1704
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2013: Localized registration of point clouds of botanic trees
A. Bucksch and Kourosh Koshelham
IEEE Geoscience and Remote Sensing Letters 10(3), pp. 631-635
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2012: GiA Roots: Software for the High Throughput Analysis of Plant Root System Architecture
T. Galkovskyi, Y. Mileyko, A. Bucksch, B. Moore, O. Symonova, C.A. Price, C.N. Topp, A.S. Iyer-Pascuzzi, P.R. Zurek, S. Fang, J. Harer, P.N. Benfey, J.S. Weitz
BMC Plant Biology 12(116)
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2011: Automated detection of branch dimensions in woody skeletons of fruit tree canopies
A. Bucksch, S. Fleck
Photogrammetric Engineering & Remote Sensing 77(3), pp. 229-240
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2010: SkelTre - Robust skeleton extraction from imperfect point clouds
A. Bucksch, R. Lindenbergh, M. Menenti
The Visual Computer 26(10), pp. 1283-1300
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2008: 3D Laser imaging as a valuable tool to specify changes in breast shape after augmentation mammaplasty
D.L. Esme, A. Bucksch, Werner H. Beekman
Aesthetic Plastic Surgery 33(2), pp. 191-195
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2008: CAMPINO - A skeletonization method for point cloud processing
A. Bucksch and R. Lindenbergh
ISPRS Journal of Photogrammetry and Remote Sensing 63(1), pp. 115-127
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2022: S. Binder, M. Yang, V. Qiu, A. Bucksch, M. Fok: Groundwater Level Remote Monitoring Using Optical Power Measurement in Fiber Bragg Grating. 2022 Optical Fiber Communications Conference and Exhibition. 6-10 March 2022, San Diego, CA.
2022: P. Pietrzyk, N. Phan-Udom, C. Chutoe, P. Saengwilai, A. Bucksch: DIRT/mu: Automatic root hair measurement in maize (Zea mays ssp.) from microscopy images. 2022 NAPPN Conference, 22-25 February 2022, Athens, GA.
2022: J. Knapp-Wilson, R. Bohn-Reckziegel, A. Bucksch, D.J. Chavez: 3D phenotyping of peach tree canopy architecture using terrestrial laser scanning. 2022 NAPPN Conference, 22-25 February 2022, Athens, GA.
2022: S. Liu, W.P. Bonelli, P. Pietrzyk, A. Bucksch: Comparison of open-source image-based reconstruction pipelines for 3D root phenotyping of field-grown maize. 2022 NAPPN Conference, 22-25 February 2022, Athens, GA.
2022: S. Binder, M. Yang, V. Qiu, A. Bucksch, M. Fok: Non-destructive measurements of root traits and their soil-water environment using Fiber Bragg Grating-based fiber optic sensors. 2022 NAPPN Conference, 22-25 February 2022, Athens, GA.
2022: L.G. Swartz, S. Liu, D. Dahlquist, E.S. Walter, S. Mcinturf, A. Bucksch, D.G. Mendoza-Cozatl: Tracking dynamic changes of leaves in response to nutrient availability using an open-source cloud-based phenotyping system (OPEN Leaf). 2022 NAPPN Conference, 22-25 February 2022, Athens, GA
2011: Characterizing tree growth anomaly induced by landslides using LiDAR
K.A. Razak, A. Bucksch, M. Damen, C. van Westen, M. Straatsma, S. de Jong
2nd World Landslide Forum, 3-9 october 2011, Rome, Italy.
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2009: Skeltre - Fast skeletonization of imperfect point clouds of botanic trees
A. Bucksch, R. Lindenbergh, M. Menenti
3D Object Retrieval Workshop/ Eurographics 2009, Munchen 28.March-3.April 2009
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2009: Automated detection of branch dimensions in woody skeletons of leafless fruit tree canopies
A. Bucksch, S. Fleck
SilviLaser 2009 proceedings, 14.-16. October 2009 Austin,Texas
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2009: A new method for individual tree measurement from airborne LiDAR
M.Z.A. Rahman, B.G.H. Gorte & A.K. Bucksch
SilviLaser 2009 proceedings, 14.-16. October 2009 Austin,Texas
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2009: A new method for individual tree delineation and undergrowth removal from high resolution airborne LiDAR
M.Z.A. Rahman, B.G.H. Gorte & A.K. Bucksch
ISPRS Workshop on Laser Scanning 2009, 1.-2. September 2009 Paris, France
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2007: Error budget of terrestrial laser scanning: Influence of the intensity remission of the scan quality
A. Bucksch, R. Lindenbergh, and J. van Ree
Proceedings of the III International Scientific Congress Geo-Siberia 2007, 23-27 April, Novosibirsk, Vol. I, 2nd part,, Geodesy, Geoinformatics, Cartography, Markscheider, pp. 113-122, ISBN 978-5-87693-229-7 and ISBN 978-5-87693-231-0
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2013: K. A. Razak, A. Bucksch, M. Straatsma, C. J. Van Westen, R. A. Bakar, S. M. de Jong. High density airborne LiDAR estimation of disrupted trees induced by landslides. IEEE IGARSS 2013, Melbourne, Australia.
Paper: DOWNLOAD
Poster:DOWNLOAD
2010: Woody biovolume extraction from laser scanned trees
A. Bucksch, S. Fleck, S. Rumpf, P. Rademacher
In Proceedings Silvilaser 2010, 14-17 September 2010, Freiburg Germany. DOWNLOAD
2009: Skeleton-based botanic tree diameter estimation from dense LiDAR data
A. Bucksch, R. Lindenbergh, M. Menenti, M. Z. A. Raman
at Opticts and Photonics 2009, San Diego(CA). In Lidar Remote Sensing for Environmental Monitoring X, edited by Upendra N. Singh, Proceedings of SPIE Vol. 7460 (SPIE, Bellingham, WA 2009) 746007.
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2009: Structural monitoring of Tunnels using terrestrial laser scanning
R. Lindenbergh, L. Uchanski, A. Bucksch, R. van Gosliga
Reports of Geodesy, Special Issue of the IX Konferencji naukowo-technicznej "Aktualne Problemy w Geodezji Inżynieryjnej”, 27./28. March 2009 in Warsawa
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2009: Applications for point cloud skeletonization in forestry and agriculture
A. Bucksch, R. Lindenbergh
Reports of Geodesy, Special Issue of the IX Konferencji naukowo-technicznej "Aktualne Problemy w Geodezji Inżynieryjnej”, 27./28. March 2009 in Warsawa
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2007: Error budget of terrestrial laser scanning: Influence of the incidence angle on the scan quality
S. Soudarissanane, J. van Ree, A. Bucksch and R. Lindenbergh,
Proceedings 3D-NordOst, 10. Anwendungsbezogener Workshop zur Erfassung, Modellierung, Verarbeitung und Auswertung von 3D-Daten, Berlin, 06./07. December 2007
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2007: 3D Buildings modeling Based on a combination of techniques and methodologies
G. Pop, A. Bucksch, B.G.H. Gorte
XXI CIPA International Symposium, 1-6 October 2007,Athens, Greece p. 1-5
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2007: Combining modern techniques for urban 3D modeling
G. Pop, A. Bucksch
IEEE International Geoscience and Remote Sensing Symposium pp. 1-4, 23- 27 July 2007, Barcelona, Spain.
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2006: Skeletonization and segmentation of point clouds using octrees and graph theory
A. Bucksch, H. Appel van Wageningen
ISPRS Symposium: Image Engineering and Vision
Metrology Vol. XXXVI. ISPRS Commission V Symposium (pp. 1-6). Dresden: Dresden University of Technology.
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2011: Revealing the skeleton from imperfect point clouds
A. Bucksch
PhD Thesis at TU Delft. Advisers: Roderik Lindenbergh and Massimo Menenti. Publisher: Dr.Hut, Munich, 2011. ISBN 978-3-86853-877-9.
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2005: Development of an integrated algorithm for surface reconstruction and point reduction in point clouds (in german)
A. Bucksch
Master Thesis at BTU Cottbus. Adviser: Winfried Kurth, February 2005
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