Difference between revisions of "Whole Brain Connectivity Atlas"
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== About == | == About == | ||
| + | [[File:S1wiring.png|200px|thumb|Diagram of S1 cortical and subcortical projections (from Zakiewicz et al., 2011, PLoS One, 6(8):e22669)]]The Whole Brain Connectivity Atlas is an interactive resource providing access to experimental tract-tracing data, showing the brain-wide distribution of efferent axonal connections originating in the rat primary somatosensory cortex. The atlas contains the results from six experiments in which an anterograde tracer, either biotinylated dextran amine (BDA) or Phaseolus vulgaris leucoagglutinin (Pha-L), was injected in the SI forelimb or whisker representations in M1. Re-use of data from these repositories is allowed provided that reference is given to original publications as specified below.[[File:2Dviewer.png|200px|thumb|2-D-image "filmstrip" viewer]] | ||
| − | + | == 2-D image repository == | |
| − | + | T'''<nowiki/>'''he 2-D image repository contains ~1200 coronal microscopic images showing data from 6 axonal tracing experiments. Image show distribution of BDA or Pha-L labeling, cytoarchitectural features (Neutral red or thinone counterstain), or chemoarchitecture in S1 (cytochrome oxidase staining). Bregma values are based on comparison with The Rat Brain in Stereotaxic Coordinates (Paxinos and Watson, 2007, Elsevier). The virtual microscopy viewer allows interactive zooming and panning. Original images are available for download via separate link. | |
| − | == | ||
| − | </ | ||
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| + | '''Re-use of data from this repository is allowed provided that reference is given to the following publication''': Zakiewicz IM, van Dongen YC, Leergaard TB, Bjaalie JG (2011) Workflow and atlas system for brain-wide mapping of axonal connectivity in rat. PLoS ONE 2011;6(8):e22669. | ||
| − | + | {| class="wikitable" | |
| − | + | !Injection site cartoon | |
| − | + | !Injected S1 region, tracer (case#) | |
| − | + | !Image repository | |
| − | + | !Experimental details | |
| − | + | !Download images | |
| − | + | |- | |
| − | + | |[[File:R601.png|75px|center]] | |
| − | + | |S1/M1 forelimb, BDA (R601) | |
| − | + | |[http://cmbn-navigator.uio.no/navigator/filmstrip/index.html?blockId=1941 Filmstrip viewer] | |
| − | + | |[[media:Metadata R601.pdf|Details (pdf)]] | |
| − | + | |[http://cmbn-navigator.uio.no/navigator/feeder/all_originals/?id=1941 R601 (tiff)] | |
| − | + | |- | |
| − | + | ||[[File:R602.png|75px|center]] | |
| − | + | |S1 whisker D2, BDA (R602) | |
| − | + | |[http://cmbn-navigator.uio.no/navigator/filmstrip/index.html?blockId=1961 Filmstrip viewer] | |
| − | + | |[[media:Metadata R602.pdf|Details (pdf)]] | |
| − | {| | + | |[http://cmbn-navigator.uio.no/navigator/feeder/all_originals/?id=1961 R602 (tiff)] |
| + | |- | ||
| + | ||[[File:R603.png|75px|center]] | ||
| + | |S1 forelimb, BDA (R603) | ||
| + | |[http://cmbn-navigator.uio.no/navigator/filmstrip/index.html?blockId=1981 Filmstrip viewer] | ||
| + | |[[media:Metadata R603.pdf|Details (pdf)]] | ||
| + | |[http://cmbn-navigator.uio.no/navigator/feeder/all_originals/?id=1981 R603 (tiff)] | ||
| + | |- | ||
| + | |[[File:R604.png|75px|center]] | ||
| + | |S1 whisker D3, BDA (R604) | ||
| + | |[http://cmbn-navigator.uio.no/navigator/filmstrip/index.html?blockId=2001 Filmstrip viewer] | ||
| + | |[[media:Metadata R604.pdf|Details (pdf)]] | ||
| + | |[http://cmbn-navigator.uio.no/navigator/feeder/all_originals/?id=2001 R604 (tiff)] | ||
| + | |- | ||
| + | |[[File:R605.png|75px|center]] | ||
| + | |S1 forelimb, Pha-L (R605) | ||
| + | |[http://cmbn-navigator.uio.no/navigator/filmstrip/index.html?blockId=2002 Filmstrip viewer] | ||
| + | |[[media:Metadata R605.pdf|Details (pdf)]] | ||
| + | |[http://cmbn-navigator.uio.no/navigator/feeder/all_originals/?id=2002 R605 (tiff)] | ||
| + | |- | ||
| + | |[[File:R606.png|75px|center]] | ||
| + | |S1 whisker D5, Pha-L (R606) | ||
| + | |[http://cmbn-navigator.uio.no/navigator/filmstrip/index.html?blockId=2003 Filmstrip viewer] | ||
| + | |[[media:Metadata R606.pdf|Details (pdf)]] | ||
| + | |[http://cmbn-navigator.uio.no/navigator/feeder/all_originals/?id=2003 R606 (tiff)] | ||
| + | |- | ||
| + | |} | ||
| + | {| class="wikitable" | ||
| + | !Filename abbreviations | ||
| + | !Description | ||
| + | |- | ||
| + | |CO | ||
| + | |Cytochrome oxidase | ||
| + | |- | ||
| + | |BDA_ABC | ||
| + | |Biotinylated dextran amine, ABC method | ||
| + | |- | ||
| + | |BDA_ABC_NR | ||
| + | |Biotinylated dextran amine, ABC method, counterstained with Neutral Red | ||
| + | |- | ||
| + | |Pha-L_PAP | ||
| + | |Phaseolus vulgaris leucoagglutinin, PAP method | ||
|- | |- | ||
| − | | | + | |Pha-L_PAP_thio |
| − | + | |Phaseolus vulgaris leucoagglutinin, PAP method, counterstained with thionine | |
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| − | | | ||
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|- | |- | ||
| − | | | + | |Pha-L_ABC |
| − | + | |Phaseolus vulgaris leucoagglutinin, ABC method | |
| − | |||
| − | | | ||
| − | |||
| − | |||
|- | |- | ||
| − | | | + | |Pha-L_ABC_thio |
| − | + | |Phaseolus vulgaris leucoagglutinin, ABC method, counterstained with thionine | |
| + | |} | ||
| + | [[File:3Dviewer.png|200px|thumb|3-D image viewer]] | ||
| − | + | == 3-D image repository == | |
| − | + | The 3-D image repository contains volumetric reconstructions of the histological images from 4 of the tract-tracing experiments available in the 2-D image repository. Technical details are provided in Zakiwicz et al. (2015, PLoS One, 10(9):e0137571), while the experimental material is described in Zakiewicz et al. (2011, PLoS One, 6(8):e22669), see also 2-D image repository. The histology volumes can be inspected in online viewer tools or downloaded as Neuroimaging Informatics Technology Initiative (NIfTI) format images for offline viewing or analysis. | |
| + | '''Re-use of data from this repository is allowed provided that reference is given to the following publication:''' Zakiewicz IM, Majka P, Wójcik DK, Bjaalie JG, Leergaard TB. Three-dimensional histology volume reconstruction of axonal tract tracing data: exploring topographical organization in subcortical projections from rat barrel cortex. PLoS ONE, 10(9):e0137571. | ||
| + | {| class="wikitable" | ||
| + | !Injection site cartoon | ||
| + | !Injected S1 region, tracer (case#) | ||
| + | !3-D image repository | ||
| + | !Experimental details | ||
| + | !Download image volume | ||
|- | |- | ||
| − | | | + | |[[File:R601.png|75px|center]] |
| − | + | |S1/M1 forelimb, BDA (R601) | |
| − | + | |[http://cmbn-navigator.uio.no/navigator/papaya/index.html?id=36037 3-D viewer] | |
| − | | | + | |[[media:Metadata R601.pdf|Details (pdf)]] |
| − | + | |[http://cmbn-navigator.uio.no/navigator/feeder/original/?id=36037 R601 (nii) 566mb] | |
| − | |||
|- | |- | ||
| − | | | + | ||[[File:R602.png|75px|center]] |
| − | + | |S1 whisker, BDA (R602) | |
| − | + | |[http://cmbn-navigator.uio.no/navigator/papaya/index.html?id=36038 3-D viewer] | |
| − | | | + | |[[media:Metadata R602.pdf|Details (pdf)]] |
| − | + | |[http://cmbn-navigator.uio.no/navigator/feeder/original/?id=36038 R602 (nii) 566mb] | |
| − | |||
|- | |- | ||
| − | | | + | ||[[File:R603.png|75px|center]] |
| − | + | |S1 forelimb, BDA (R603) | |
| − | + | |[http://cmbn-navigator.uio.no/navigator/papaya/index.html?id=36039 3-D viewer] | |
| − | | | + | |[[media:Metadata R603.pdf|Details (pdf)]] |
| − | + | |[http://cmbn-navigator.uio.no/navigator/feeder/original/?id=36039 R603 (nii) 566mb] | |
| − | |||
|- | |- | ||
| − | | | + | |[[File:R604.png|75px|center]] |
| − | + | |S1 whisker, BDA (R604) | |
| − | + | |[http://cmbn-navigator.uio.no/navigator/papaya/index.html?id=36040 3-D viewer] | |
| − | | | + | |[[media:Metadata R604.pdf|Details (pdf)]] |
| − | + | |[http://cmbn-navigator.uio.no/navigator/feeder/original/?id=36040 R604 (nii) 566mb] | |
| − | |||
|- | |- | ||
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|} | |} | ||
| − | + | == Experimental procedures in brief == | |
| − | + | Tract-tracing experiments were conducted in four adult Sprague Dawley rats and two adult Wistar rats. In each animal, an anterograde axonal tracer (biotinylated dextran amine, BDA or Phaseolus vulgaris leucoagglutinin, Pha-L) was iontophoretically injected in the whisker or forelimb representation of SI (five cases) or MI (one case). Coronal brain sections were stained to visualize BDA or Pha-L and counterstained to visualize cytoarchitectural features. Selected sections were stained for cytochrome oxidase to visualize the characteristic SI barrel organization. Images were obtained through an automated Olympus Bx52 microscope, equipped with a high-precision motorized stage running the Neurolucida v6.0 Virtual Slice software (MicroBrightField Inc., Williston, VT, USA). Serial image were assigned anterio-posterior Bregma coordinates by identification of anatomical landmarks and comparison with a rat brain atlas (The Rat Brain In Stereotaxic Coordinates, Paxinos and Watson, 2007). For further details about tract-tracing experiments and the 2-D image repository, see Zakiewicz et al., 2011, PLoS One, 6(8):e22669). For methodological details about 3-D histological reconstructions, see Zakiewicz et al., 2015, PLoS One, 10(9):e0137571). | |
| − | == | ||
| − | + | == History == | |
| − | + | * 2015-09 - 3-D image repository launched (Zakiewicz et al., PloS One, 2015, 10(9):e0137571) | |
| − | + | * 2015-09 - Wiki pages established, new filmstrip viewer system | |
| + | * 2014-02 - Analysis of brain-wide distribution of S1 efferent projections (Zakiewicz et al., Front Neuroinf 2014; doi: 10.3389/fninf.2014.00005) | ||
| + | * 2011-07 - 2-D image repository launched (Zakiewicz et al., PLoS One 2011;6(8):e22669) | ||
| + | * 2009-09 - Poster/demo, 2nd INCF Congress of Neuroinformatics, Plzen, Czech Republic | ||
| − | == | + | == Documentation == |
| + | * Zakiewicz IM, Majka P, Wojcik DK, Bjaalie JG, Leergaard TB (2015) Three-dimensional histology volume reconstruction of axonal tract tracing data: exploring topographical organization in subcortical projections from rat barrel cortex. PloS One; 10(9):e0137571. | ||
| + | * Zakiewicz IM, Bjaalie JG, Leergaard TB (2014) Brain-wide map of efferent projections from rat barrel cortex, Front. Neuroinform 8:5, doi: 10.3389/fninf.2014.00005 | ||
| + | * Zakiewicz IM, van Dongen YC, Leergaard TB, Bjaalie JG (2011) Workflow and atlas system for brain-wide mapping of axonal connectivity in rat. PLoS One; 6(8):e22669. doi: 10.1371/journal.pone.0022669 | ||
| + | * Moene IA, Subramaniam S, Darine D, Leergaard TB, Bjaalie JG (2007). Towards a workbench for rodent brain image data: systems architecture and design. Neuroinformatics; 5: 35-58 | ||
| + | * Bjaalie JG, Leergaard TB, Lillehaug S, Odeh F, Moene IA, Kjøde JO, Darine D (2005) Database and tools for analysis of topographic organization and map transformations in major projection systems of the brain. Neuroscience; 136:681-696 | ||
| − | + | == Atlas development team == | |
| + | '''Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo''' | ||
| + | * Izabela M. Zakiewicz | ||
| + | * Yvette C. van Dongen | ||
| + | * Jan Olav Kjøde | ||
| + | * Ivar Andre Moene | ||
| + | * Gergely Csucs | ||
| + | * Dmitri Darine | ||
| + | * Trygve B. Leergaard | ||
| + | * Jan G. Bjaalie | ||
| − | + | == Funded by: == | |
| − | + | * EMBIO/MLS@UIO (PS-V08, http://www.uio.no/forskning/tverrfak/mls/om/) | |
| + | * The Research Council of Norway (Norwegian Node of the International Neuroinformatics Coordinating Facility, project ID 214842, http://www.forskningsradet.no) | ||
| + | * Human Brain Project through the European Union Seventh Framework Program (FP7/2007-2013) under grant agreement no. 604102 (HBP) | ||
| + | * https://www.humanbrainproject.eu/) | ||
| − | == | + | == Contributing laboratories == |
| − | + | * '''Neural Systems Laboratory '''([http://www.nesys.uio.no) http://www.nesys.uio.no]), Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, Department of Anatomy, University of Oslo, P.O. Box 1105 Blindern, N - 0317 Oslo, Norway: ''Experimental work, brain-wide mapping, atlas repository. '' | |
| − | + | * '''Laboratory of Neuroinformatics''' (http://en.nencki.gov.pl/laboratory-of-neuroinformatics), Department of Neurophysiology, Nencki Institute of Experimental Biology, 02-093 Warszawa, Poland: ''3-D histology volume reconstructions'' | |
| − | |||
| − | |||
| − | == | + | == Contact == |
| − | + | * j.g.bjaalie@medisin.uio.no | |
| − | |||
Latest revision as of 19:09, 16 February 2021
Contents
About
The Whole Brain Connectivity Atlas is an interactive resource providing access to experimental tract-tracing data, showing the brain-wide distribution of efferent axonal connections originating in the rat primary somatosensory cortex. The atlas contains the results from six experiments in which an anterograde tracer, either biotinylated dextran amine (BDA) or Phaseolus vulgaris leucoagglutinin (Pha-L), was injected in the SI forelimb or whisker representations in M1. Re-use of data from these repositories is allowed provided that reference is given to original publications as specified below.
2-D image repository
The 2-D image repository contains ~1200 coronal microscopic images showing data from 6 axonal tracing experiments. Image show distribution of BDA or Pha-L labeling, cytoarchitectural features (Neutral red or thinone counterstain), or chemoarchitecture in S1 (cytochrome oxidase staining). Bregma values are based on comparison with The Rat Brain in Stereotaxic Coordinates (Paxinos and Watson, 2007, Elsevier). The virtual microscopy viewer allows interactive zooming and panning. Original images are available for download via separate link.
Re-use of data from this repository is allowed provided that reference is given to the following publication: Zakiewicz IM, van Dongen YC, Leergaard TB, Bjaalie JG (2011) Workflow and atlas system for brain-wide mapping of axonal connectivity in rat. PLoS ONE 2011;6(8):e22669.
| Injection site cartoon | Injected S1 region, tracer (case#) | Image repository | Experimental details | Download images |
|---|---|---|---|---|
 |
S1/M1 forelimb, BDA (R601) | Filmstrip viewer | Details (pdf) | R601 (tiff) |
 |
S1 whisker D2, BDA (R602) | Filmstrip viewer | Details (pdf) | R602 (tiff) |
 |
S1 forelimb, BDA (R603) | Filmstrip viewer | Details (pdf) | R603 (tiff) |
 |
S1 whisker D3, BDA (R604) | Filmstrip viewer | Details (pdf) | R604 (tiff) |
 |
S1 forelimb, Pha-L (R605) | Filmstrip viewer | Details (pdf) | R605 (tiff) |
 |
S1 whisker D5, Pha-L (R606) | Filmstrip viewer | Details (pdf) | R606 (tiff) |
| Filename abbreviations | Description |
|---|---|
| CO | Cytochrome oxidase |
| BDA_ABC | Biotinylated dextran amine, ABC method |
| BDA_ABC_NR | Biotinylated dextran amine, ABC method, counterstained with Neutral Red |
| Pha-L_PAP | Phaseolus vulgaris leucoagglutinin, PAP method |
| Pha-L_PAP_thio | Phaseolus vulgaris leucoagglutinin, PAP method, counterstained with thionine |
| Pha-L_ABC | Phaseolus vulgaris leucoagglutinin, ABC method |
| Pha-L_ABC_thio | Phaseolus vulgaris leucoagglutinin, ABC method, counterstained with thionine |
3-D image repository
The 3-D image repository contains volumetric reconstructions of the histological images from 4 of the tract-tracing experiments available in the 2-D image repository. Technical details are provided in Zakiwicz et al. (2015, PLoS One, 10(9):e0137571), while the experimental material is described in Zakiewicz et al. (2011, PLoS One, 6(8):e22669), see also 2-D image repository. The histology volumes can be inspected in online viewer tools or downloaded as Neuroimaging Informatics Technology Initiative (NIfTI) format images for offline viewing or analysis.
Re-use of data from this repository is allowed provided that reference is given to the following publication: Zakiewicz IM, Majka P, Wójcik DK, Bjaalie JG, Leergaard TB. Three-dimensional histology volume reconstruction of axonal tract tracing data: exploring topographical organization in subcortical projections from rat barrel cortex. PLoS ONE, 10(9):e0137571.
| Injection site cartoon | Injected S1 region, tracer (case#) | 3-D image repository | Experimental details | Download image volume |
|---|---|---|---|---|
|
S1/M1 forelimb, BDA (R601) | 3-D viewer | Details (pdf) | R601 (nii) 566mb |
|
S1 whisker, BDA (R602) | 3-D viewer | Details (pdf) | R602 (nii) 566mb |
|
S1 forelimb, BDA (R603) | 3-D viewer | Details (pdf) | R603 (nii) 566mb |
|
S1 whisker, BDA (R604) | 3-D viewer | Details (pdf) | R604 (nii) 566mb |
Experimental procedures in brief
Tract-tracing experiments were conducted in four adult Sprague Dawley rats and two adult Wistar rats. In each animal, an anterograde axonal tracer (biotinylated dextran amine, BDA or Phaseolus vulgaris leucoagglutinin, Pha-L) was iontophoretically injected in the whisker or forelimb representation of SI (five cases) or MI (one case). Coronal brain sections were stained to visualize BDA or Pha-L and counterstained to visualize cytoarchitectural features. Selected sections were stained for cytochrome oxidase to visualize the characteristic SI barrel organization. Images were obtained through an automated Olympus Bx52 microscope, equipped with a high-precision motorized stage running the Neurolucida v6.0 Virtual Slice software (MicroBrightField Inc., Williston, VT, USA). Serial image were assigned anterio-posterior Bregma coordinates by identification of anatomical landmarks and comparison with a rat brain atlas (The Rat Brain In Stereotaxic Coordinates, Paxinos and Watson, 2007). For further details about tract-tracing experiments and the 2-D image repository, see Zakiewicz et al., 2011, PLoS One, 6(8):e22669). For methodological details about 3-D histological reconstructions, see Zakiewicz et al., 2015, PLoS One, 10(9):e0137571).
History
- 2015-09 - 3-D image repository launched (Zakiewicz et al., PloS One, 2015, 10(9):e0137571)
- 2015-09 - Wiki pages established, new filmstrip viewer system
- 2014-02 - Analysis of brain-wide distribution of S1 efferent projections (Zakiewicz et al., Front Neuroinf 2014; doi: 10.3389/fninf.2014.00005)
- 2011-07 - 2-D image repository launched (Zakiewicz et al., PLoS One 2011;6(8):e22669)
- 2009-09 - Poster/demo, 2nd INCF Congress of Neuroinformatics, Plzen, Czech Republic
Documentation
- Zakiewicz IM, Majka P, Wojcik DK, Bjaalie JG, Leergaard TB (2015) Three-dimensional histology volume reconstruction of axonal tract tracing data: exploring topographical organization in subcortical projections from rat barrel cortex. PloS One; 10(9):e0137571.
- Zakiewicz IM, Bjaalie JG, Leergaard TB (2014) Brain-wide map of efferent projections from rat barrel cortex, Front. Neuroinform 8:5, doi: 10.3389/fninf.2014.00005
- Zakiewicz IM, van Dongen YC, Leergaard TB, Bjaalie JG (2011) Workflow and atlas system for brain-wide mapping of axonal connectivity in rat. PLoS One; 6(8):e22669. doi: 10.1371/journal.pone.0022669
- Moene IA, Subramaniam S, Darine D, Leergaard TB, Bjaalie JG (2007). Towards a workbench for rodent brain image data: systems architecture and design. Neuroinformatics; 5: 35-58
- Bjaalie JG, Leergaard TB, Lillehaug S, Odeh F, Moene IA, Kjøde JO, Darine D (2005) Database and tools for analysis of topographic organization and map transformations in major projection systems of the brain. Neuroscience; 136:681-696
Atlas development team
Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo
- Izabela M. Zakiewicz
- Yvette C. van Dongen
- Jan Olav Kjøde
- Ivar Andre Moene
- Gergely Csucs
- Dmitri Darine
- Trygve B. Leergaard
- Jan G. Bjaalie
Funded by:
- EMBIO/MLS@UIO (PS-V08, http://www.uio.no/forskning/tverrfak/mls/om/)
- The Research Council of Norway (Norwegian Node of the International Neuroinformatics Coordinating Facility, project ID 214842, http://www.forskningsradet.no)
- Human Brain Project through the European Union Seventh Framework Program (FP7/2007-2013) under grant agreement no. 604102 (HBP)
- https://www.humanbrainproject.eu/)
Contributing laboratories
- Neural Systems Laboratory (http://www.nesys.uio.no), Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, Department of Anatomy, University of Oslo, P.O. Box 1105 Blindern, N - 0317 Oslo, Norway: Experimental work, brain-wide mapping, atlas repository.
- Laboratory of Neuroinformatics (http://en.nencki.gov.pl/laboratory-of-neuroinformatics), Department of Neurophysiology, Nencki Institute of Experimental Biology, 02-093 Warszawa, Poland: 3-D histology volume reconstructions
Contact
- j.g.bjaalie@medisin.uio.no
