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wiki:biomedical_image_analysis [2015/04/15 17:09]
Alessandro G
wiki:biomedical_image_analysis [2018/10/09 03:23] (current)
Alessandro G [Mitosis Detection in Breast Cancer Histology Images using Deep Neural Networks]
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 ===== Mitosis Detection in Breast Cancer Histology Images using Deep Neural Networks ===== ===== Mitosis Detection in Breast Cancer Histology Images using Deep Neural Networks =====
-Joint work with [[http://​www.idsia.ch/​~dan|Dan Ciresan]].+Joint work with [[http://​www.idsia.ch/​~ciresan|Dan Ciresan]].
  
 == News: == == News: ==
-  * **Nov, 2014**: The Medical Image Analysis paper describing the MICCAI 2013 Grand Challenge "​[[http://​amida13.isi.uu.nl/​|Assessment of Mitosis Detection Algorithms]]"​ has been accepted ([[http://​arxiv.org/​pdf/​1411.5825v1.pdf|preprint]],​ [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25547073|pubmed]],​ [[http://​arxiv.org/​abs/​1411.5825|arxiv]]). +  * Our research was featured in the widely popular [[https://​www.youtube.com/​watch?​v=Bui3DWs02h4|two minute papers]] youtube channel! 
-  * **Sept, 2013**: With [[http://​www.idsia.ch/​~ciresan|Dan Ciresan]], we won the MICCAI 2013 Grand Challenge "​[[http://​amida13.isi.uu.nl/​|Assessment of Mitosis Detection Algorithms]]",​ with a significant advantage over the closest competitor ([[http://​amida13.isi.uu.nl/?​q=node/​62|results]]).  +  * The Medical Image Analysis paper describing the MICCAI 2013 Grand Challenge "​[[http://​amida13.isi.uu.nl/​|Assessment of Mitosis Detection Algorithms]]"​ has been accepted ([[http://​arxiv.org/​pdf/​1411.5825v1.pdf|preprint]],​ [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25547073|pubmed]],​ [[http://​arxiv.org/​abs/​1411.5825|arxiv]]). 
-  * **Oct, 2012**: ​With [[http://​www.idsia.ch/​~ciresan|Dan Ciresan]], we won the ICPR 2012 challenge on [[http://​ipal.cnrs.fr/​ICPR2012/​|mitosis detection]] in breast cancer histology images. ​ The paper describing the approach was published at MICCAI 2013.+  * The user testing website for the paper "A Comparison of Algorithms and Humans for Mitosis Detection"​ is online. [[http://​bit.ly/​YUYQFG|Take the test]]! 
 +  * With [[http://​www.idsia.ch/​~ciresan|Dan Ciresan]], we won the MICCAI 2013 Grand Challenge "​[[http://​amida13.isi.uu.nl/​|Assessment of Mitosis Detection Algorithms]]",​ with a significant advantage over the closest competitor ([[http://​amida13.isi.uu.nl/?​q=node/​62|results]]).  
 +  * With [[http://​www.idsia.ch/​~ciresan|Dan Ciresan]], we won the ICPR 2012 challenge on [[http://​ipal.cnrs.fr/​ICPR2012/​|mitosis detection]] in breast cancer histology images. ​ The paper describing the approach was published at MICCAI 2013.
  
 {{ :​wiki:​biomed-mitosis.jpg?​nolink&​900 |}} {{ :​wiki:​biomed-mitosis.jpg?​nolink&​900 |}}
  
 == Related Publications:​ == == Related Publications:​ ==
-  * A. Giusti, C. Caccia, D. Ciresan, J. Schmidhuber,​ L. Gambardella:​ “A Comparison of Algorithms and Humans for Mitosis Detection”. Proc. of International Symposium on Biomedical Imaging (ISBI) 2014. (**oral presentation**)+  * A. Giusti, C. Caccia, D. Ciresan, J. Schmidhuber,​ L. Gambardella:​ “A Comparison of Algorithms and Humans for Mitosis Detection”. Proc. of International Symposium on Biomedical Imaging (ISBI) 2014. **oral presentation**. ([[http://​www.idsia.ch/​~ciresan/​data/​isbi2014.pdf|preprint]],​ [[http://​bit.ly/​YUYQFG|take the test]])
   * D. Ciresan, A. Giusti, L. Gambardella,​ J. Schmidhuber:​ “Mitosis Detection in Breast Cancer Histology Images with Deep Neural Networks”. Proc. of International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2013. **Describing our winning entry to ICPR 2012 Mitosis Detection competition**. ([[http://​www.idsia.ch/​~ciresan/​data/​miccai2013.pdf|preprint]],​ [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24579167|pubmed]])   * D. Ciresan, A. Giusti, L. Gambardella,​ J. Schmidhuber:​ “Mitosis Detection in Breast Cancer Histology Images with Deep Neural Networks”. Proc. of International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2013. **Describing our winning entry to ICPR 2012 Mitosis Detection competition**. ([[http://​www.idsia.ch/​~ciresan/​data/​miccai2013.pdf|preprint]],​ [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24579167|pubmed]])
   * M. Veta et al.: "​Assessment of algorithms for mitosis detection in breast cancer histopathology images"​. Medical Image Analysis (accepted). ([[http://​arxiv.org/​pdf/​1411.5825v1.pdf|preprint]],​ [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25547073|pubmed]],​ [[http://​arxiv.org/​abs/​1411.5825|arxiv]]).   * M. Veta et al.: "​Assessment of algorithms for mitosis detection in breast cancer histopathology images"​. Medical Image Analysis (accepted). ([[http://​arxiv.org/​pdf/​1411.5825v1.pdf|preprint]],​ [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25547073|pubmed]],​ [[http://​arxiv.org/​abs/​1411.5825|arxiv]]).
 +  * M. Veta, P. J. van Diest, D. Ciresan, A. Giusti, J. Pluim: “Prognostic value of automatic mitosis detection in breast cancer histopathology images”. Proc. of International Symposium on Biomedical Imaging (ISBI) 2015. (abstract).
  
  
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 } }
 </​code>​ </​code>​
- 
 ===== Segmentation of Neural Structures from Electron Microscopy Stacks using Deep Neural Networks ===== ===== Segmentation of Neural Structures from Electron Microscopy Stacks using Deep Neural Networks =====
-Joint work with [[http://​www.idsia.ch/​~dan|Dan Ciresan]] and other colleagues at MIT, Janelia Farm, and ETH.+Joint work with [[http://​www.idsia.ch/​~ciresan|Dan Ciresan]] and other colleagues at MIT, Janelia Farm, and ETH.
  
 == News: == == News: ==
-  * **Mar, 2012**: ​With [[http://​www.idsia.ch/​~ciresan|Dan Ciresan]], we won (by a large margin) the ISBI 2012 [[http://​brainiac2.mit.edu/​isbi_challenge/​content/​isbi-2012-workshop-results|challenge]] on segmentation of neuronal structures in electron microscopy stacks. Our entry outperforms all the 16 competing methods on each of the three considered metrics. ​ In addition, we are the only entry outperforming humans in the pixel error metric. ​ We published our approach at NIPS 2012.+  * With [[http://​www.idsia.ch/​~ciresan|Dan Ciresan]], we won (by a large margin) the ISBI 2012 [[http://​brainiac2.mit.edu/​isbi_challenge/​content/​isbi-2012-workshop-results|challenge]] on segmentation of neuronal structures in electron microscopy stacks. Our entry outperforms all the 16 competing methods on each of the three considered metrics. ​ In addition, we are the only entry outperforming humans in the pixel error metric. ​ We published our approach at NIPS 2012.
  
 {{ :​wiki:​biomed-neurons.jpg?​nolink&​900 |}} {{ :​wiki:​biomed-neurons.jpg?​nolink&​900 |}}
  
 == Related Publications == == Related Publications ==
-  * J. Funke, et al.: “Candidate Sampling for Neuron Reconstruction from Anisotropic Electron Microscopy Volumes”. Proc. of International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2014 
   * D. Ciresan, A. Giusti, L. Gambardella,​ J. Schmidthuber:​ “Deep Neural Networks Segment Neuronal Membranes in Electron Microscopy Images”. Proc. of International Conference on Neural Information Processing Systems (NIPS) 2012 (**acceptance rate ~25%**).   * D. Ciresan, A. Giusti, L. Gambardella,​ J. Schmidthuber:​ “Deep Neural Networks Segment Neuronal Membranes in Electron Microscopy Images”. Proc. of International Conference on Neural Information Processing Systems (NIPS) 2012 (**acceptance rate ~25%**).
-  * D. Ciresan, A. Giusti, L. Gambardella,​ J. Schmidthuber:​ “Neural Networks for Segmenting Neuronal Structures in EM Stacks”. **Describing our winning entry (in all three metrics) for ISBI 2012 competition “Segmentation of neuronal structures in EM stacks”**.+  ​* T. Parag, D. Ciresan, A. Giusti: “Efficient Classifier Training to Reduce False Merges in Electron Microscopy Segmentation”. Proc. of International Conference on Computer Vision (ICCV) 2015 
 +  * I. Arganda-Carreras et al.: "​Crowdsourcing the creation of image segmentation algorithms for connectomics"​. 
 +Frontiers in Neuroanatomy 2015. ([[http://​dx.doi.org/​10.3389/​fnana.2015.00142|DOI Link]]) 
 +  * J. Funke, et al.: “Candidate Sampling for Neuron Reconstruction from Anisotropic Electron Microscopy Volumes”. Proc. of International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2014 
 +  ​* D. Ciresan, A. Giusti, L. Gambardella,​ J. Schmidthuber:​ “Neural Networks for Segmenting Neuronal Structures in EM Stacks”. **Describing our winning entry (in all three metrics) for ISBI 2012 competition “Segmentation of neuronal structures in EM stacks”**, Workshop at International Symposium on Biomedical Imaging (ISBI) 2012.
  
 == Bibtex == == Bibtex ==
 <​code>​ <​code>​
 +
 +@inproceedings{Parag:​2015,​
 +  title={Efficient Classifier Training to Reduce False Merges in Electron Microscopy Segmentation},​
 +  author={Parag,​ Toufiq and Cire{\c{s}}an,​ Dan C and Giusti, Alessandro},​
 +  booktitle={ICCV},​
 +  year={2015}
 +}
 +
 +@inproceedings{Funke:​2014,​
 +  title={Candidate Sampling for Neuron Reconstruction from Anisotropic Electron Microscopy Volumes},
 +  author={Funke,​ Jan and Martel, Julien NP and Gerhard, Stephan and Andres, Bjoern and Cire{\c{s}}an,​ Dan C and Giusti, Alessandro and Gambardella,​ Luca M and Schmidhuber,​ J{\"​u}rgen and Pfister, Hanspeter and Cardona, Albert and others},
 +  booktitle={Medical Image Computing and Computer-Assisted Intervention--MICCAI 2014},
 +  pages={17--24},​
 +  year={2014},​
 +  publisher={Springer}
 +}
 +
 @inproceedings{Ciresan:​2012f,​ @inproceedings{Ciresan:​2012f,​
   author ​   = {Dan Claudiu Ciresan and   author ​   = {Dan Claudiu Ciresan and
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 } }
 </​code>​ </​code>​
- 
 ===== Image Analysis (and Statistical Modeling) for Human Embryo Grading ===== ===== Image Analysis (and Statistical Modeling) for Human Embryo Grading =====
 Joint work with [[http://​www.idsia.ch/​~giorgio|Giorgio Corani]] and the [[http://​www.iirm.ch|International Institute of Reproductive Medicine in Lugano, Switzlerland]]. Joint work with [[http://​www.idsia.ch/​~giorgio|Giorgio Corani]] and the [[http://​www.iirm.ch|International Institute of Reproductive Medicine in Lugano, Switzlerland]].