3D reconstruction and standardization of the rat vibrissal cortex for precise registration of single neuron morphology.
The three-dimensional (3D) structure of neural circuits is commonly studied by reconstructing individual or small groups of neurons in separate preparations. Investigation of structural organization principles or quantification of dendritic and axonal innervation thus requires integration of many re...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002837&type=printable |
| _version_ | 1826799439325429760 |
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| author | Robert Egger Rajeevan T Narayanan Moritz Helmstaedter Christiaan P J de Kock Marcel Oberlaender |
| author_facet | Robert Egger Rajeevan T Narayanan Moritz Helmstaedter Christiaan P J de Kock Marcel Oberlaender |
| author_sort | Robert Egger |
| collection | DOAJ |
| description | The three-dimensional (3D) structure of neural circuits is commonly studied by reconstructing individual or small groups of neurons in separate preparations. Investigation of structural organization principles or quantification of dendritic and axonal innervation thus requires integration of many reconstructed morphologies into a common reference frame. Here we present a standardized 3D model of the rat vibrissal cortex and introduce an automated registration tool that allows for precise placement of single neuron reconstructions. We (1) developed an automated image processing pipeline to reconstruct 3D anatomical landmarks, i.e., the barrels in Layer 4, the pia and white matter surfaces and the blood vessel pattern from high-resolution images, (2) quantified these landmarks in 12 different rats, (3) generated an average 3D model of the vibrissal cortex and (4) used rigid transformations and stepwise linear scaling to register 94 neuron morphologies, reconstructed from in vivo stainings, to the standardized cortex model. We find that anatomical landmarks vary substantially across the vibrissal cortex within an individual rat. In contrast, the 3D layout of the entire vibrissal cortex remains remarkably preserved across animals. This allows for precise registration of individual neuron reconstructions with approximately 30 µm accuracy. Our approach could be used to reconstruct and standardize other anatomically defined brain areas and may ultimately lead to a precise digital reference atlas of the rat brain. |
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| format | Article |
| id | doaj.art-f0973d7dc1b94adb87fca2311c6f5479 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2025-03-17T00:35:06Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS Computational Biology |
| spelling | doaj.art-f0973d7dc1b94adb87fca2311c6f54792025-02-21T05:32:03ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582012-01-01812e100283710.1371/journal.pcbi.10028373D reconstruction and standardization of the rat vibrissal cortex for precise registration of single neuron morphology.Robert EggerRajeevan T NarayananMoritz HelmstaedterChristiaan P J de KockMarcel OberlaenderThe three-dimensional (3D) structure of neural circuits is commonly studied by reconstructing individual or small groups of neurons in separate preparations. Investigation of structural organization principles or quantification of dendritic and axonal innervation thus requires integration of many reconstructed morphologies into a common reference frame. Here we present a standardized 3D model of the rat vibrissal cortex and introduce an automated registration tool that allows for precise placement of single neuron reconstructions. We (1) developed an automated image processing pipeline to reconstruct 3D anatomical landmarks, i.e., the barrels in Layer 4, the pia and white matter surfaces and the blood vessel pattern from high-resolution images, (2) quantified these landmarks in 12 different rats, (3) generated an average 3D model of the vibrissal cortex and (4) used rigid transformations and stepwise linear scaling to register 94 neuron morphologies, reconstructed from in vivo stainings, to the standardized cortex model. We find that anatomical landmarks vary substantially across the vibrissal cortex within an individual rat. In contrast, the 3D layout of the entire vibrissal cortex remains remarkably preserved across animals. This allows for precise registration of individual neuron reconstructions with approximately 30 µm accuracy. Our approach could be used to reconstruct and standardize other anatomically defined brain areas and may ultimately lead to a precise digital reference atlas of the rat brain.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002837&type=printable |
| spellingShingle | Robert Egger Rajeevan T Narayanan Moritz Helmstaedter Christiaan P J de Kock Marcel Oberlaender 3D reconstruction and standardization of the rat vibrissal cortex for precise registration of single neuron morphology. PLoS Computational Biology |
| title | 3D reconstruction and standardization of the rat vibrissal cortex for precise registration of single neuron morphology. |
| title_full | 3D reconstruction and standardization of the rat vibrissal cortex for precise registration of single neuron morphology. |
| title_fullStr | 3D reconstruction and standardization of the rat vibrissal cortex for precise registration of single neuron morphology. |
| title_full_unstemmed | 3D reconstruction and standardization of the rat vibrissal cortex for precise registration of single neuron morphology. |
| title_short | 3D reconstruction and standardization of the rat vibrissal cortex for precise registration of single neuron morphology. |
| title_sort | 3d reconstruction and standardization of the rat vibrissal cortex for precise registration of single neuron morphology |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002837&type=printable |
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