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Analyzing multi-tag bioimages with BioIMAX colocation mining tools

Jan Kolling, Magnus Rathke, Dominic Gardner, Tim W. Nattkemper, Sylvie Abouna, Michael Khan
2012 2012 9th IEEE International Symposium on Biomedical Imaging (ISBI)  
The application of multi-tag protocols in fluorescence microscopy allows the visualization of a large number (> 10) of molecules (i. e. proteins) in a sample (like a tissue section). However, the analysis of such high dimensional bioimages is a difficult task for most of the labs, since software solutions for particular data mining steps are difficult to use or just not available. In this paper we present two new free online tools: MICOLT (Multivariate Image COlocation Tool) and MIFIST
more » ... iate Image Frequent Item Set Tool). Both tools can be used via our recently proposed online bioimage analysis platform BioIMAX, so users can upload their bioimage data, apply the tools and share the results with other invited users based on BioIMAX' concept of shared virtual projects. Data mining with these tools includes the computation and visualization colocation factors well established in the microscopy community (like Mander's score) and association rule mining following the frequent item set principle, thereby supporting large and small scale analysis.
doi:10.1109/isbi.2012.6235802 dblp:conf/isbi/KollingRGNAK12 fatcat:7y5cay4ctzg6zml6snvogqvtzu

Computer Aided Detection of Polyps in Whitelight- Colonoscopy Images using Deep Neural Networks

Thomas Wittenberg, Pascal Zobel, Magnus Rathke, Steffen Mühldorfer
2019 Current Directions in Biomedical Engineering  
Early detection of polyps is one central goal of colonoscopic screening programs. To support gastroenterologists during this examination process, deep convolutional neural network can be applied for computer-assisted detection of neoplastic lesions. In this work, a Mask R-CNN architecture was applied. For training and testing, three independent colonoscopy data sets were used, including 2484 HD labelled images with polyps from our clinic, as well as two public image data sets from the MICCAI
more » ... 5 polyp detection challenge, consisting of 612 SD and 194 HD labelled images with polyps. After training the deep neural network, best results for the three test data sets were achieved in the range of recall = 0.92, precision = 0.86, F1 = 0.89 (data set A), rec = 0.86, prec = 0.80, F1 = 0.82 (data set B) and rec = 0.83, prec = 0.74, F1 = 0.79 (data set C).
doi:10.1515/cdbme-2019-0059 fatcat:gjjmkfmxrncqljcjbvadue77ti

Towards computer aided diagnosis of infective endocarditis in whole-slide images of heart valve tissue using FISH

Volker Bruns, Daniela Franz, Petr Kuritcyn, Veit Wiesmann, Magnus Rathke, Thomas Wittenberg, Alexandra Wießner, Laura Kursawe, Annette Moter, Judith Kikhney, Christian Münzenmayer
2021 Current Directions in Biomedical Engineering  
D Franz, P Kuritcyn, C Münzenmayer, M Rathke, V Wiesmann, T Wittenberg: Fraunhofer IIS, Erlangen; J Kikhney, L Kursawe, A Wießner, A Moter: Charité-University Medicine Berlin, Germany, MoKi Analytics GmbH  ...  D Franz, P Kuritcyn, C Münzenmayer, M Rathke, V Wiesmann, T Wittenberg: Fraunhofer IIS, Erlangen; J Kikhney, L Kursawe, A Wießner, A Moter: Charité-University Medicine Berlin, Germany, MoKi Analytics GmbH  ... 
doi:10.1515/cdbme-2021-2119 fatcat:tdkekjmedva2thyoj7fptwe3pu


2007 Kritische Justiz  
Erhellende Interviews mit Horst Herold (ehemaliger Präsident des Bundeskriminal- amtes) und Hans Magnus Enzensberger schließen das Werk ab.  ...  Angesichts dieser Ausgangsparameter hat Rathke vom Grundansatz her den Versuch des großen, weit ausholenden Wurfs gewagt.  ... 
doi:10.5771/0023-4834-2007-3-312 fatcat:755a4gwcs5eoncxtelriuzvifa

Page 226 of Nature Vol. 1, Issue 8 [page]

1869 Nature  
Rathke on Molecular Combinations. Ladenburg on the Molecular Weight of certain Protoxides and Protochlo- rides. Fleury on the Action of Pentachloride of Phosphorus on Phenolic Ethers.  ...  Vice-presidents: Pro- fessors Baeyer, Hoffmann, Magnus, and Rose. Secretaries and Vice-Secretaries: Dr. Eichermann, Dr. Martius, Dr. Oppenheim, and Dr. Wichelhaus. Treasurer: Mr. Scherinn.  ... 

Check list of species (algae, invertebrates and vertebrates) found in the vicinity of the island of helgoland (North Sea, German Bight) — a review of recent records

J. Harms
1993 Helgoländer Meeresuntersuchungen  
Rhodophyceae Ahnfeltia plicata (Hudson) Fries Antithamnion ptumula (Ellis) Thur. in Le Jolis Audouinella membranacea (Magnus) Papenfuss Bangia atropurpurea (Roth) C. Ag.  ...  Cheirocratus sundevallii (Rathke, 1843) Corophium crassicorne Bruzelius, 1859 Corophium insidosum Crawford, 1937 Corophium sextoni Crawford, 1937 Corophium sp.  ... 
doi:10.1007/bf02366182 fatcat:irjneak22fag3kd2stu7iejoam

LXXIX. Notices respecting new books

1837 The London Edinburgh and Dublin Philosophical Magazine and Journal of Science  
Magnus.  ...  Rathke.--Contributions to the knowledge of the Trilobites, with especial regard to their definite number of Members ; by A. Quenstedt.--On the genus Proeyon; by Prof. Wiegmann.--Fossil quadrumana.  ... 
doi:10.1080/14786443708649349 fatcat:f3yk6r5hyrbbtm3rvpf2o5pgha

Page 92 of Forest and Stream; A Journal of Outdoor Life, Travel, Nature Study, Shooting, Fishing, Yachting Vol. 18, Issue 5 [page]

1882 Forest and Stream; A Journal of Outdoor Life, Travel, Nature Study, Shooting, Fishing, Yachting  
Mitiller | as the young eels, claiming that the eel should be considered | nor Rathke, but really Carlo Mondini was the first discov- as an animal which brought forth its young alive, although | erer,  ...  principal supporters of the theory that the ecl was ] eels in a tub on the deck of a vessel while on Lake Ontario, | There are at least four distinct types, resulting from the | viviparous were Alburtus Magnus  ... 

The institution of semiotics in Estonia

Kalevi Kull, Silvi Salupere, Peeter Torop, Mihhail Lotman
2011 Sign Systems Studies  
semiotics which was established in 1820, has been headed by Jean Jacques Friedrich Wilhelm Parrot (1791 -1841 ) in 1821 -1826 , by Johann Friedrich Erdmann (1778 -1846 ) in 1827 -1828 , by Martin Heinrich Rathke  ...  Zoosemiotic work included observations in Tallinn Zoo (Aleksei Turovski, Timo Maran), as well as the analysis of dog training (Riin Magnus).  ... 
doi:10.12697/sss.2011.39.2-4.13 fatcat:ejqz677gc5fmtnhujoit6msng4

Further information on the oribatid fauna (Acarina, Oribatei) of the northern palearctic region: Ukraina and Czechoslovakia

Eero Karppinen, V. Melamud, Ladislav Miko, Dimitri Krivolutsky
1992 Entomologica Fennica  
Koch, 184 1): 4, 5, 9, 12, 15, 23-25, 34, 34a, 35, 39, 45, 48, 52, 53, 55, 55a,56,57,67, 71 -R. duplicata (Grandjean, 1953 ): 3, 4, 8, 34, 34a,35,52,55,55a, 71,75 -R. loricata (Rathke, 1799 ): 38 HYPOCHTHONIIDAE  ...  Steganacarus Ewing, 1917 -S. applicatus (Sellnick, 1920 ): 21, 23, 66,71 S. carinatus (C.L.Koch, 1841 ): 1-5,7-13, 15, 18-24, 26-29 , 30a, 33, 34, 34a, 38, 39, 41-45,47,48,53,56-58,66,67 , 74 , 75 S. magnus  ... 
doi:10.33338/ef.83570 fatcat:6mzqytpnijb3pdb5aeotcy5eoa

On the Ones Who Hear the Whistle: Towards an Analytical Framework for Analysing Complaint Recipients

Selina Rathke
2018 MaRBLe  
., 2014; Read & Rama, 2003) . 1 Selina Rathke received a bachelor of arts degree in European Studies at Maastricht University in 2018.  ...  Mazerolle & Brown, 2008; Mesmer-Magnus & Viswesvaran, 2005; Moberly, 2014) . Despite their importance, so far only few whistleblowing studies focus explicitly on complaint recipients (e.g.  ... 
doi:10.26481/marble.2018.v4.644 fatcat:q5zadttjwnal7pulqzonteaoo4

La physiologie française pendant la première moitié du XIXe siècle

Georgette Legée
1988 Gesnerus  
E. von Baer (1858); Carus G.G. (1859); Rathke H. (1793-1860), en 1860; K.von Siebold, physiologiste (1804-1885), en 1867.  ...  Gmelin et Tiedemann, Magnus et Bischoff^réalisent des expériences pour trouver une explication valable, mais les résultats manquent de rigueur. Cependant Magnus s'approche d'une solution positive.  ... 
doi:10.1163/22977953-04502005 fatcat:fwyt54ols5ak7c2qreino34e3i

Preliminary observations on the mandibles of palaemonoid shrimp (Crustacea: Decapoda: Caridea: Palaemonoidea)

Christopher W. Ashelby, Sammy De Grave, Magnus L. Johnson
2015 PeerJ  
The semi-rigid, robust mandible has usually been attributed a solely mechanical function in the breaking down of food prior to ingestion, but a recent study of larval Palaemon elegans Rathke, 1837 demonstrated  ...  Magnus L. Johnson is an Academic Editor for PeerJ. Author Contributions • Christopher W.  ...  . • Magnus L. Johnson analyzed the data, wrote the paper, reviewed drafts of the paper.  ... 
doi:10.7717/peerj.846 pmid:25825676 pmcid:PMC4375974 fatcat:fn2lcvzufvduzcft6gywo2l5cq


1903 The Lancet  
BRUCE showed a woman suffering mainly from Paralysis of the Right Serratus Magnus Muscle.  ...  There was also a case in a sheep described by Rathke in 1830 in which a female foetus was attached to the head of a male foetus by an umbilical cord which passed into the skull and ended in a wellformed  ... 
doi:10.1016/s0140-6736(01)39227-9 fatcat:bgzuqwy3rvab7ooghj3vjsqw2a

The "De Ovorum Gallinaceorum Generationis Primo Exordio, Etc." of Volcher Coiter (Part II, Conclusion)

Howard B Adelmann
1933 Annals of medical history  
Albertus Magnus: (Ref. 95, Lib. vi, tract 1, cap. 4: 37.) 89.  ...  Not until the middle of the nineteenth century, and then only through the combined labors of Wolff, Pander, von Baer, Reichert, Rathke, Schwann, Bischoff, Remak, KoIIiker and others were the early stages  ... 
pmid:33944230 pmcid:PMC7945431 fatcat:4c2ynsddofga3jxgpp3infawgi
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