Automated cell nucleus detection for large-volume electron microscopy of neural tissue

2014 IEEE 11th International Symposium on Biomedical Imaging, ISBI 2014

Volumn , Issue , 2014, Pages 69-72

  Tek, F Boray ^a   Kroeger, Thorben ^b   Mikula, Shawn ^c   Hamprecht, Fred A ^b  

^a ISIK UNIVERSITY   (Turkey)

^b UNIVERSITY OF HEIDELBERG   (Germany)

^c MAX PLANCK INSTITUTE FOR MEDICAL RESEARCH   (Germany)

Author keywords

Automated nucleus detection; Block face electron microscopy; Block wise connected components; Connectomics; Interactive segmentation; Random forest; Soma

Indexed keywords

AUTOMATION; BRAIN; CELLS; CYTOLOGY; DECISION TREES; ELECTRON MICROSCOPES; ELECTRON MICROSCOPY; ELECTRONS; MEDICAL IMAGING;

CONNECTED COMPONENT; CONNECTOMICS; INTERACTIVE SEGMENTATION; RANDOM FORESTS; SOMA;

LARGE DATASET;

EID: 84927539855     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/isbi.2014.6867811     Document Type: Conference Paper

References (10)

1. W. Denk and H. Horstmann, "Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanos-tructure," PLoS biology, Vol. 2, no. 11, pp. e329, 2004.
2. M. Oberlaender, V. J. Dercksen, R. Egger, et al., "Automated three-dimensional detection and counting of neuron somata," J. Neurosci. Meth., Vol. 180, no. 1, pp. 147-160, 2009.
3. P. S. Tsai, J. P. Kaufhold, P. Blinder, et al., "Correlations of neuronal and microvascular densities in murine cortex revealed by direct counting and colocalization of nuclei and vessels," Journal of Neuroscience, Vol. 29, no. 46, pp. 14553-14570, 2009.
4. S. Mikula, J. Binding, and W. Denk, "Staining and embedding the whole mouse brain for electron microscopy," Nature methods, Vol. 9, no. 12, pp. 1198-1201, 2012.
5. J. Binding, S. Mikula, and W. Denk, "Low-dosage maximum-a-posteriori focusing and stigmation," Microsc. Microanal., Vol. 19, no. 01, pp. 38-55, 2013.
6. E. Ling, J. A. Paterson, A. Privat, S. Mori, and C. Leblond, "Investigation of glial cells in semithin sections. I. Identification of glial cells in the brain of young rats," J. Comp. Neurol., Vol. 149, no. 1, pp. 43-71, 1973.
7. M. Matamales, J. Bertran-Gonzalez, L. Salomon, et al., "Striatal medium-sized spiny neurons: identification by nuclear staining and study of neuronal subpopulations in BAC transgenic mice," PloS one, Vol. 4, no. 3, pp. e4770, 2009.
8. C. Sommer, C. Straehle, U. Köthe, and F. Hamprecht, "Ilastik: Interactive learning and segmentation toolkit," in ISBI, 2011, pp. 230-233.
9. A. Kreshuk, C. N. Straehle, C. Sommer, et al., "Automated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images," PloS one, Vol. 6, no. 10, pp. e24899, 2011.
10. Dataset and ground-truth annotations available at: http://hci.iwr.uni-heidelberg.de/somas