Automated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images.
We describe a protocol for fully automated detection and segmentation of asymmetric, presumed excitatory, synapses in serial electron microscopy images of the adult mammalian cerebral cortex, taken with the focused ion beam, scanning electron microscope (FIB/SEM). The procedure is based on interacti...
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Public Library of Science (PLoS)
2011
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oai:doaj.org-article:a4d430fff120405491476c69513b3ffa2021-11-18T07:35:59ZAutomated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images.1932-620310.1371/journal.pone.0024899https://doaj.org/article/a4d430fff120405491476c69513b3ffa2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22031814/?tool=EBIhttps://doaj.org/toc/1932-6203We describe a protocol for fully automated detection and segmentation of asymmetric, presumed excitatory, synapses in serial electron microscopy images of the adult mammalian cerebral cortex, taken with the focused ion beam, scanning electron microscope (FIB/SEM). The procedure is based on interactive machine learning and only requires a few labeled synapses for training. The statistical learning is performed on geometrical features of 3D neighborhoods of each voxel and can fully exploit the high z-resolution of the data. On a quantitative validation dataset of 111 synapses in 409 images of 1948×1342 pixels with manual annotations by three independent experts the error rate of the algorithm was found to be comparable to that of the experts (0.92 recall at 0.89 precision). Our software offers a convenient interface for labeling the training data and the possibility to visualize and proofread the results in 3D. The source code, the test dataset and the ground truth annotation are freely available on the website http://www.ilastik.org/synapse-detection.Anna KreshukChristoph N StraehleChristoph SommerUllrich KoetheMarco CantoniGraham KnottFred A HamprechtPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 10, p e24899 (2011) |
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DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Anna Kreshuk Christoph N Straehle Christoph Sommer Ullrich Koethe Marco Cantoni Graham Knott Fred A Hamprecht Automated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images. |
| description |
We describe a protocol for fully automated detection and segmentation of asymmetric, presumed excitatory, synapses in serial electron microscopy images of the adult mammalian cerebral cortex, taken with the focused ion beam, scanning electron microscope (FIB/SEM). The procedure is based on interactive machine learning and only requires a few labeled synapses for training. The statistical learning is performed on geometrical features of 3D neighborhoods of each voxel and can fully exploit the high z-resolution of the data. On a quantitative validation dataset of 111 synapses in 409 images of 1948×1342 pixels with manual annotations by three independent experts the error rate of the algorithm was found to be comparable to that of the experts (0.92 recall at 0.89 precision). Our software offers a convenient interface for labeling the training data and the possibility to visualize and proofread the results in 3D. The source code, the test dataset and the ground truth annotation are freely available on the website http://www.ilastik.org/synapse-detection. |
| format |
article |
| author |
Anna Kreshuk Christoph N Straehle Christoph Sommer Ullrich Koethe Marco Cantoni Graham Knott Fred A Hamprecht |
| author_facet |
Anna Kreshuk Christoph N Straehle Christoph Sommer Ullrich Koethe Marco Cantoni Graham Knott Fred A Hamprecht |
| author_sort |
Anna Kreshuk |
| title |
Automated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images. |
| title_short |
Automated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images. |
| title_full |
Automated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images. |
| title_fullStr |
Automated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images. |
| title_full_unstemmed |
Automated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images. |
| title_sort |
automated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2011 |
| url |
https://doaj.org/article/a4d430fff120405491476c69513b3ffa |
| work_keys_str_mv |
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