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Items: 44

1.

Author Correction: U-Net: deep learning for cell counting, detection, and morphometry.

Falk T, Mai D, Bensch R, Çiçek Ö, Abdulkadir A, Marrakchi Y, Böhm A, Deubner J, Jäckel Z, Seiwald K, Dovzhenko A, Tietz O, Bosco CD, Walsh S, Saltukoglu D, Tay TL, Prinz M, Palme K, Simons M, Diester I, Brox T, Ronneberger O.

Nat Methods. 2019 Feb 25. doi: 10.1038/s41592-019-0356-4. [Epub ahead of print]

PMID:
30804552
2.

U-Net: deep learning for cell counting, detection, and morphometry.

Falk T, Mai D, Bensch R, Çiçek Ö, Abdulkadir A, Marrakchi Y, Böhm A, Deubner J, Jäckel Z, Seiwald K, Dovzhenko A, Tietz O, Dal Bosco C, Walsh S, Saltukoglu D, Tay TL, Prinz M, Palme K, Simons M, Diester I, Brox T, Ronneberger O.

Nat Methods. 2019 Jan;16(1):67-70. doi: 10.1038/s41592-018-0261-2. Epub 2018 Dec 17. Erratum in: Nat Methods. 2019 Feb 25;:.

PMID:
30559429
3.

Clinically applicable deep learning for diagnosis and referral in retinal disease.

De Fauw J, Ledsam JR, Romera-Paredes B, Nikolov S, Tomasev N, Blackwell S, Askham H, Glorot X, O'Donoghue B, Visentin D, van den Driessche G, Lakshminarayanan B, Meyer C, Mackinder F, Bouton S, Ayoub K, Chopra R, King D, Karthikesalingam A, Hughes CO, Raine R, Hughes J, Sim DA, Egan C, Tufail A, Montgomery H, Hassabis D, Rees G, Back T, Khaw PT, Suleyman M, Cornebise J, Keane PA, Ronneberger O.

Nat Med. 2018 Sep;24(9):1342-1350. doi: 10.1038/s41591-018-0107-6. Epub 2018 Aug 13.

PMID:
30104768
4.

Data-Driven Modeling of Intracellular Auxin Fluxes Indicates a Dominant Role of the ER in Controlling Nuclear Auxin Uptake.

Middleton AM, Dal Bosco C, Chlap P, Bensch R, Harz H, Ren F, Bergmann S, Wend S, Weber W, Hayashi KI, Zurbriggen MD, Uhl R, Ronneberger O, Palme K, Fleck C, Dovzhenko A.

Cell Rep. 2018 Mar 13;22(11):3044-3057. doi: 10.1016/j.celrep.2018.02.074.

5.

An objective comparison of cell-tracking algorithms.

Ulman V, Maška M, Magnusson KEG, Ronneberger O, Haubold C, Harder N, Matula P, Matula P, Svoboda D, Radojevic M, Smal I, Rohr K, Jaldén J, Blau HM, Dzyubachyk O, Lelieveldt B, Xiao P, Li Y, Cho SY, Dufour AC, Olivo-Marin JC, Reyes-Aldasoro CC, Solis-Lemus JA, Bensch R, Brox T, Stegmaier J, Mikut R, Wolf S, Hamprecht FA, Esteves T, Quelhas P, Demirel Ö, Malmström L, Jug F, Tomancak P, Meijering E, Muñoz-Barrutia A, Kozubek M, Ortiz-de-Solorzano C.

Nat Methods. 2017 Dec;14(12):1141-1152. doi: 10.1038/nmeth.4473. Epub 2017 Oct 30.

6.

Automated analysis of retinal imaging using machine learning techniques for computer vision.

De Fauw J, Keane P, Tomasev N, Visentin D, van den Driessche G, Johnson M, Hughes CO, Chu C, Ledsam J, Back T, Peto T, Rees G, Montgomery H, Raine R, Ronneberger O, Cornebise J.

Version 2. F1000Res. 2016 Jul 5 [revised 2017 Jan 1];5:1573. doi: 10.12688/f1000research.8996.2. eCollection 2016.

7.

A 3D digital atlas of the Nicotiana tabacum root tip and its use to investigate changes in the root apical meristem induced by the Agrobacterium 6b oncogene.

Pasternak T, Haser T, Falk T, Ronneberger O, Palme K, Otten L.

Plant J. 2017 Oct;92(1):31-42. doi: 10.1111/tpj.13631. Epub 2017 Aug 11.

8.

A new fate mapping system reveals context-dependent random or clonal expansion of microglia.

Tay TL, Mai D, Dautzenberg J, Fernández-Klett F, Lin G, Sagar, Datta M, Drougard A, Stempfl T, Ardura-Fabregat A, Staszewski O, Margineanu A, Sporbert A, Steinmetz LM, Pospisilik JA, Jung S, Priller J, Grün D, Ronneberger O, Prinz M.

Nat Neurosci. 2017 Jun;20(6):793-803. doi: 10.1038/nn.4547. Epub 2017 Apr 17.

PMID:
28414331
9.

Gland segmentation in colon histology images: The glas challenge contest.

Sirinukunwattana K, Pluim JPW, Chen H, Qi X, Heng PA, Guo YB, Wang LY, Matuszewski BJ, Bruni E, Sanchez U, Böhm A, Ronneberger O, Cheikh BB, Racoceanu D, Kainz P, Pfeiffer M, Urschler M, Snead DRJ, Rajpoot NM.

Med Image Anal. 2017 Jan;35:489-502. doi: 10.1016/j.media.2016.08.008. Epub 2016 Sep 3. Review.

PMID:
27614792
10.

A benchmark for comparison of dental radiography analysis algorithms.

Wang CW, Huang CT, Lee JH, Li CH, Chang SW, Siao MJ, Lai TM, Ibragimov B, Vrtovec T, Ronneberger O, Fischer P, Cootes TF, Lindner C.

Med Image Anal. 2016 Jul;31:63-76. doi: 10.1016/j.media.2016.02.004. Epub 2016 Feb 28.

11.

The polarity protein Inturned links NPHP4 to Daam1 to control the subapical actin network in multiciliated cells.

Yasunaga T, Hoff S, Schell C, Helmstädter M, Kretz O, Kuechlin S, Yakulov TA, Engel C, Müller B, Bensch R, Ronneberger O, Huber TB, Lienkamp SS, Walz G.

J Cell Biol. 2015 Dec 7;211(5):963-73. doi: 10.1083/jcb.201502043.

12.

Spontaneous and electric field-controlled front-rear polarization of human keratinocytes.

Saltukoglu D, Grünewald J, Strohmeyer N, Bensch R, Ulbrich MH, Ronneberger O, Simons M.

Mol Biol Cell. 2015 Dec 1;26(24):4373-86. doi: 10.1091/mbc.E14-12-1580. Epub 2015 Sep 30.

13.

B cell antigen receptors of the IgM and IgD classes are clustered in different protein islands that are altered during B cell activation.

Maity PC, Blount A, Jumaa H, Ronneberger O, Lillemeier BF, Reth M.

Sci Signal. 2015 Sep 15;8(394):ra93. doi: 10.1126/scisignal.2005887.

PMID:
26373673
14.

Amotl2a interacts with the Hippo effector Yap1 and the Wnt/β-catenin effector Lef1 to control tissue size in zebrafish.

Agarwala S, Duquesne S, Liu K, Boehm A, Grimm L, Link S, König S, Eimer S, Ronneberger O, Lecaudey V.

Elife. 2015 Sep 3;4:e08201. doi: 10.7554/eLife.08201.

15.

The Rac1 regulator ELMO controls basal body migration and docking in multiciliated cells through interaction with Ezrin.

Epting D, Slanchev K, Boehlke C, Hoff S, Loges NT, Yasunaga T, Indorf L, Nestel S, Lienkamp SS, Omran H, Kuehn EW, Ronneberger O, Walz G, Kramer-Zucker A.

Development. 2015 Apr 15;142(8):1553. doi: 10.1242/dev.124214. No abstract available.

16.

Standardized evaluation of algorithms for computer-aided diagnosis of dementia based on structural MRI: the CADDementia challenge.

Bron EE, Smits M, van der Flier WM, Vrenken H, Barkhof F, Scheltens P, Papma JM, Steketee RM, Méndez Orellana C, Meijboom R, Pinto M, Meireles JR, Garrett C, Bastos-Leite AJ, Abdulkadir A, Ronneberger O, Amoroso N, Bellotti R, Cárdenas-Peña D, Álvarez-Meza AM, Dolph CV, Iftekharuddin KM, Eskildsen SF, Coupé P, Fonov VS, Franke K, Gaser C, Ledig C, Guerrero R, Tong T, Gray KR, Moradi E, Tohka J, Routier A, Durrleman S, Sarica A, Di Fatta G, Sensi F, Chincarini A, Smith GM, Stoyanov ZV, Sørensen L, Nielsen M, Tangaro S, Inglese P, Wachinger C, Reuter M, van Swieten JC, Niessen WJ, Klein S; Alzheimer's Disease Neuroimaging Initiative.

Neuroimage. 2015 May 1;111:562-79. doi: 10.1016/j.neuroimage.2015.01.048. Epub 2015 Jan 31.

17.

The Rac1 regulator ELMO controls basal body migration and docking in multiciliated cells through interaction with Ezrin.

Epting D, Slanchev K, Boehlke C, Hoff S, Loges NT, Yasunaga T, Indorf L, Nestel S, Lienkamp SS, Omran H, Kuehn EW, Ronneberger O, Walz G, Kramer-Zucker A.

Development. 2015 Jan 1;142(1):174-84. doi: 10.1242/dev.112250. Erratum in: Development. 2015 Apr 15;142(8):1553.

18.

Correction of inter-scanner and within-subject variance in structural MRI based automated diagnosing.

Kostro D, Abdulkadir A, Durr A, Roos R, Leavitt BR, Johnson H, Cash D, Tabrizi SJ, Scahill RI, Ronneberger O, Klöppel S; Track-HD Investigators.

Neuroimage. 2014 Sep;98:405-15. doi: 10.1016/j.neuroimage.2014.04.057. Epub 2014 Apr 29.

PMID:
24791746
19.

The iRoCS Toolbox--3D analysis of the plant root apical meristem at cellular resolution.

Schmidt T, Pasternak T, Liu K, Blein T, Aubry-Hivet D, Dovzhenko A, Duerr J, Teale W, Ditengou FA, Burkhardt H, Ronneberger O, Palme K.

Plant J. 2014 Mar;77(5):806-14. doi: 10.1111/tpj.12429. Epub 2014 Feb 12.

20.

Variational attenuation correction in two-view confocal microscopy.

Schmidt T, Dürr J, Keuper M, Blein T, Palme K, Ronneberger O.

BMC Bioinformatics. 2013 Dec 18;14:366. doi: 10.1186/1471-2105-14-366.

21.

Validation of fluorescence molecular tomography/micro-CT multimodal imaging in vivo in rats.

Vonwil D, Christensen J, Fischer S, Ronneberger O, Shastri VP.

Mol Imaging Biol. 2014 Jun;16(3):350-61. doi: 10.1007/s11307-013-0698-8.

PMID:
24163020
22.

Non-directional radial intercalation dominates deep cell behavior during zebrafish epiboly.

Bensch R, Song S, Ronneberger O, Driever W.

Biol Open. 2013 Jun 3;2(8):845-54. doi: 10.1242/bio.20134614. eCollection 2013 Aug 15.

23.

Automated processing of zebrafish imaging data: a survey.

Mikut R, Dickmeis T, Driever W, Geurts P, Hamprecht FA, Kausler BX, Ledesma-Carbayo MJ, Marée R, Mikula K, Pantazis P, Ronneberger O, Santos A, Stotzka R, Strähle U, Peyriéras N.

Zebrafish. 2013 Sep;10(3):401-21. doi: 10.1089/zeb.2013.0886. Epub 2013 Jun 12. Review.

24.

Semi-automatic determination of cell surface areas used in systems biology.

Morath V, Keuper M, Rodriguez-Franco M, Deswal S, Fiala G, Blumenthal B, Kaschek D, Timmer J, Neuhaus G, Ehl S, Ronneberger O, Schamel WW.

Front Biosci (Elite Ed). 2013 Jan 1;5:533-45.

PMID:
23277009
25.

Vertebrate kidney tubules elongate using a planar cell polarity-dependent, rosette-based mechanism of convergent extension.

Lienkamp SS, Liu K, Karner CM, Carroll TJ, Ronneberger O, Wallingford JB, Walz G.

Nat Genet. 2012 Dec;44(12):1382-7. doi: 10.1038/ng.2452. Epub 2012 Nov 11.

26.

Shroom3 is required downstream of FGF signalling to mediate proneuromast assembly in zebrafish.

Ernst S, Liu K, Agarwala S, Moratscheck N, Avci ME, Dalle Nogare D, Chitnis AB, Ronneberger O, Lecaudey V.

Development. 2012 Dec;139(24):4571-81. doi: 10.1242/dev.083253. Epub 2012 Nov 7.

27.

Influence of cell-to-cell variability on spatial pattern formation.

Greese B, Wester K, Bensch R, Ronneberger O, Timmer J, Huulskamp M, Fleck C.

IET Syst Biol. 2012 Aug;6(4):143-53. doi: 10.1049/iet-syb.2011.0050.

PMID:
23039695
28.

Functional and structural MRI biomarkers to detect pre-clinical neurodegeneration.

Abdulkadir A, Ronneberger O, Wolf RC, Pfleiderer B, Saft C, Klöppel S.

Curr Alzheimer Res. 2013 Feb;10(2):125-34.

PMID:
22742852
29.

ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains.

Ronneberger O, Liu K, Rath M, Rueβ D, Mueller T, Skibbe H, Drayer B, Schmidt T, Filippi A, Nitschke R, Brox T, Burkhardt H, Driever W.

Nat Methods. 2012 Jun 17;9(7):735-42. doi: 10.1038/nmeth.2076. Erratum in: Nat Methods. 2012 Oct;9(10):1031.

PMID:
22706672
30.

Multiview deblurring for 3-D images from light-sheet-based fluorescence microscopy.

Temerinac-Ott M, Ronneberger O, Ochs P, Driever W, Brox T, Burkhardt H.

IEEE Trans Image Process. 2012 Apr;21(4):1863-73. doi: 10.1109/TIP.2011.2181528. Epub 2011 Dec 23.

PMID:
22203719
31.

Fast rotation invariant 3D feature computation utilizing efficient local neighborhood operators.

Skibbe H, Reisert M, Schmidt T, Brox T, Ronneberger O, Burkhardt H.

IEEE Trans Pattern Anal Mach Intell. 2012 Aug;34(8):1563-75.

PMID:
22201055
32.

A comparison of different automated methods for the detection of white matter lesions in MRI data.

Klöppel S, Abdulkadir A, Hadjidemetriou S, Issleib S, Frings L, Thanh TN, Mader I, Teipel SJ, Hüll M, Ronneberger O.

Neuroimage. 2011 Jul 15;57(2):416-22. doi: 10.1016/j.neuroimage.2011.04.053. Epub 2011 May 3.

PMID:
21569857
33.
34.

Inversin relays Frizzled-8 signals to promote proximal pronephros development.

Lienkamp S, Ganner A, Boehlke C, Schmidt T, Arnold SJ, Schäfer T, Romaker D, Schuler J, Hoff S, Powelske C, Eifler A, Krönig C, Bullerkotte A, Nitschke R, Kuehn EW, Kim E, Burkhardt H, Brox T, Ronneberger O, Gloy J, Walz G.

Proc Natl Acad Sci U S A. 2010 Nov 23;107(47):20388-93. doi: 10.1073/pnas.1013070107. Epub 2010 Nov 8.

35.

Harmonic filters for 3D multichannel data: rotation invariant detection of mitoses in colorectal cancer.

Schlachter M, Reisert M, Herz C, Schlürmann F, Lassmann S, Werner M, Burkhardt H, Ronneberger O.

IEEE Trans Med Imaging. 2010 Aug;29(8):1485-95. doi: 10.1109/TMI.2010.2049856. Epub 2010 Jun 7.

PMID:
20529733
36.

Early functional magnetic resonance imaging activations predict language outcome after stroke.

Saur D, Ronneberger O, Kümmerer D, Mader I, Weiller C, Klöppel S.

Brain. 2010 Apr;133(Pt 4):1252-64. doi: 10.1093/brain/awq021. Epub 2010 Mar 18.

PMID:
20299389
37.

Rotational invariance based on Fourier analysis in polar and spherical coordinates.

Wang Q, Ronneberger O, Burkhardt H.

IEEE Trans Pattern Anal Mach Intell. 2009 Sep;31(9):1715-22. doi: 10.1109/TPAMI.2009.29.

PMID:
19574630
38.

XuvTools: free, fast and reliable stitching of large 3D datasets.

Emmenlauer M, Ronneberger O, Ponti A, Schwarb P, Griffa A, Filippi A, Nitschke R, Driever W, Burkhardt H.

J Microsc. 2009 Jan;233(1):42-60. doi: 10.1111/j.1365-2818.2008.03094.x.

39.

Spatial quantitative analysis of fluorescently labeled nuclear structures: problems, methods, pitfalls.

Ronneberger O, Baddeley D, Scheipl F, Verveer PJ, Burkhardt H, Cremer C, Fahrmeir L, Cremer T, Joffe B.

Chromosome Res. 2008;16(3):523-62. doi: 10.1007/s10577-008-1236-4. Review.

PMID:
18461488
40.

On-line monitoring and identification of bioaerosols.

Rösch P, Harz M, Peschke KD, Ronneberger O, Burkhardt H, Schüle A, Schmauz G, Lankers M, Hofer S, Thiele H, Motzkus HW, Popp J.

Anal Chem. 2006 Apr 1;78(7):2163-70.

PMID:
16579594
41.

Identification of single eukaryotic cells with micro-Raman spectroscopy.

Rösch P, Harz M, Peschke KD, Ronneberger O, Burkhardt H, Popp J.

Biopolymers. 2006 Jul;82(4):312-6.

PMID:
16421914
42.

Classification of lactic acid bacteria with UV-resonance Raman spectroscopy.

Gaus K, Rösch P, Petry R, Peschke KD, Ronneberger O, Burkhardt H, Baumann K, Popp J.

Biopolymers. 2006 Jul;82(4):286-90.

PMID:
16421858
43.

Micro-Raman spectroscopic identification of bacterial cells of the genus Staphylococcus and dependence on their cultivation conditions.

Harz M, Rösch P, Peschke KD, Ronneberger O, Burkhardt H, Popp J.

Analyst. 2005 Nov;130(11):1543-50. Epub 2005 Sep 30.

PMID:
16222378
44.

Chemotaxonomic identification of single bacteria by micro-Raman spectroscopy: application to clean-room-relevant biological contaminations.

Rösch P, Harz M, Schmitt M, Peschke KD, Ronneberger O, Burkhardt H, Motzkus HW, Lankers M, Hofer S, Thiele H, Popp J.

Appl Environ Microbiol. 2005 Mar;71(3):1626-37.

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