This collection contains histology images of the macaque basal ganglia: [sample_id: pU01BGsMFrSNiCM067d210714tNISSLn1, Corresponding slide-seq samples: pU01BGsMFrSNiCM067d210701tSLIDESEQnPuck_210528_02 ; pU01BGsMFrSNiCM067d210701tSLIDESEQnPuck_210528_03 ; pU01BGsMFrSNiCM067d210701tSLIDESEQnPuck_210528_04, Total number sets: 5], [sample_id: pU01BGsMFrSNiCM067d210714tNISSLn2, Corresponding slide-seq samples: pU01BGsMFrSNiCM067d210701tSLIDESEQnPuck_210528_05 ; pU01BGsMFrSNiCM067d210701tSLIDESEQnPuck_210528_08 ; pU01BGsMFrSNiCM067d210701tSLIDESEQnPuck_210528_09, Total number sets: 5], [sample_id: pU01BGsMFrSNiCM067d210714tNISSLn3, Corresponding slide-seq samples: pU01BGsMFrSNiCM067d210701tSLIDESEQnPuck_210528_10 ; pU01BGsMFrSNiCM067d210701tSLIDESEQnPuck_210528_14 ; pU01BGsMFrSNiCM067d210701tSLIDESEQnPuck_210528_18, Total number sets: 5, POST image is missing], [sample_id: pU01BGsMFrSNiCM067d210714tNISSLn4, Corresponding slide-seq samples: pU01BGsMFrSNiCM067d210701tSLIDESEQnPuck_210528_32 ; pU01BGsMFrSNiCM067d210701tSLIDESEQnPuck_210528_33, Total number sets: 5, PRE image is missing], [sample_id: pU01BGsMFrSNiCM067d210714tNISSLn5, Corresponding slide-seq samples: pU01BGsMFrSNiCM067d210701tSLIDESEQnPuck_210528_34 ; pU01BGsMFrSNiCM067d210701tSLIDESEQnPuck_210528_35 ; pU01BGsMFrSNiCM067d210701tSLIDESEQnPuck_210528_36, Total number sets: 5], [sample_id: pU01BGsMFrSNiCM068d210910tNISSLn1, Corresponding slide-seq samples: pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210716_01 ; pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210716_02 ; pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210716_03, Total number sets: 7], [sample_id: pU01BGsMFrSNiCM068d210910tNISSLn2, Corresponding slide-seq samples: pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210716_04 ; pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210716_06 ; pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210716_07, Total number sets: 7], [sample_id: pU01BGsMFrSNiCM068d210910tNISSLn3, Corresponding slide-seq samples: pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210716_08 ; pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210716_09 ; pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210716_11, Total number sets: 7], [sample_id: pU01BGsMFrSNiCM068d210910tNISSLn4, Corresponding slide-seq samples: pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210716_12 ; pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210716_13 ; pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210716_14, Total number sets: 7], [sample_id: pU01BGsMFrSNiCM068d210910tNISSLn5, Corresponding slide-seq samples: pU01BGsMFrSNiCM068d210818tSLIDESEQLnPuck_210716_16 ; pU01BGsMFrSNiCM068d210818tSLIDESEQLnPuck_210716_17 ; pU01BGsMFrSNiCM068d210818tSLIDESEQLnPuck_210720_01, Total number sets: 7, POST image is missing], [sample_id: pU01BGsMFrSNiCM068d210910tNISSLn6, Corresponding slide-seq samples: pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210720_02 ; pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210720_03 ; pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210720_04, Total number sets: 7], [sample_id: pU01BGsMFrSNiCM068d210910tNISSLn7, Corresponding slide-seq samples: pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210720_06 ; pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210720_07 ; pU01BGsMFrSNiCM068d210818tSLIDESEQnPuck_210720_08, Total number sets: 7]

Investigator
Evan Macosko
Macosko Lab
Broad Institute
Funding
1-U01-MH124602-01

Experiment
Modality: histology imaging
Method: Nissl stain
Technique: histology
Structure: substantia nigra
Organism: crab-eating macaque
TransLine: None
Cells: None

BIL: /bil/data/6e/33/6e33a6c22d6e960a/pU01BGsMFrSNiCM067d210714tNISSLn4/
HTTPS: https://download.brainimagelibrary.org/6e/33/6e33a6c22d6e960a/pU01BGsMFrSNiCM067d210714tNISSLn4/

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Background - Autofluorescence
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0459/LSFM/Background
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0459/LSFM/Background

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Neurotrace Fluorescent Stain
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0456/LSFM/Neurotrace
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0456/LSFM/Neurotrace

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Neurotrace Fluorescent Stain
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0138/LSFM/Neurotrace
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0138/LSFM/Neurotrace

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Background - Autofluorescence
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0452/LSFM/Background
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0452/LSFM/Background

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Syto16 Fluorescent protein antibody labelling
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0138/LSFM/Syto16
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0138/LSFM/Syto16

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Lectin Fluorescent Stain
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E11-5_BB0444/LSFM/Lectin
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E11-5_BB0444/LSFM/Lectin

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Lectin Fluorescent Stain
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0459/LSFM/Lectin
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0459/LSFM/Lectin

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Lectin Fluorescent Stain
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0439/LSFM/Lectin
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0439/LSFM/Lectin

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Background2 - Autofluorescence
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0454/LSFM/Background2
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0454/LSFM/Background2

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Lectin Fluorescent Stain
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E11-5_BB0380/LSFM/Lectin
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E11-5_BB0380/LSFM/Lectin

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Background - Autofluorescence
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0453/LSFM/Background
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0453/LSFM/Background

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Neurotrace Fluorescent Stain
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0340/LSFM/Neurotrace
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0340/LSFM/Neurotrace

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Neurotrace Fluorescent Stain
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0341/LSFM/Neurotrace
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0341/LSFM/Neurotrace

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Background - Autofluorescence
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E11-5_BB0380/LSFM/Background
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E11-5_BB0380/LSFM/Background

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Neurotrace Fluorescent Stain
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0452/LSFM/Neurotrace
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0452/LSFM/Neurotrace

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Lectin Fluorescent Stain
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0455/LSFM/Lectin
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0455/LSFM/Lectin

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Background2 - Autofluorescence
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0452/LSFM/Background2
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0452/LSFM/Background2

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Background - Autofluorescence
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0341/LSFM/Background
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0341/LSFM/Background

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Background - Autofluorescence
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0454/LSFM/Background
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0454/LSFM/Background

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Neurotrace Fluorescent Stain
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0453/LSFM/Neurotrace
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0453/LSFM/Neurotrace

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Background - Autofluorescence
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0456/LSFM/Background
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0456/LSFM/Background

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Lectin Fluorescent Stain
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0341/LSFM/Lectin
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0341/LSFM/Lectin

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Neurotrace Fluorescent Stain
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E13-5_BB0454/LSFM/Neurotrace
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E13-5_BB0454/LSFM/Neurotrace

Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing, complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. Common coordinate frameworks (CCF) provide an essential spatial context with which to understand cell type composition and 3D arrangement in the mouse brain. For the adult mouse brain, the Allen CCF currently serves as a standard atlas resource with which to map and integrate results from different studies. On the other hand, the lack of CCFs in developing mouse brains significantly impedes progress on quantitative spatiotemporal understanding of cell types during neurodevelopment. To address this deficiency, we intend to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we utilize MRI, light sheet fluorescent microscopy (LSFM), and Serial Two Photon Tomography (STPT) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features highlighted, including total cell density, myelination, and neurovasculature. Second, we will create fully 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain. This specific data submission collected during 2021Q4 includes a variety of LSFM data from ages E11.5 and E13.5, MRI datasets from ages P4 and E15.5, and STPT datasets from P4, P14, and P56.

Investigator
Yongsoo Kim
Yongsoo Kim Lab
Pennsylvania State University
Funding
1-RF1-MH124605-01

Experiment
Modality: histology imaging
Method: Lectin Fluorescent Stain
Technique: light sheet microscopy
Structure: whole brain
Organism: mouse
TransLine: C57BL/6
Cells: 0

BIL: /bil/data/0d/89/0d89ff2f52ee3323/E11-5_BB0378/LSFM/Lectin
HTTPS: https://download.brainimagelibrary.org/0d/89/0d89ff2f52ee3323/E11-5_BB0378/LSFM/Lectin