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Brain-wide distribution of reporter expression in five transgenic tetracycline-transactivator mouse lines.

Scientific data | 2019

The spatial pattern of transgene expression in tetracycline-controlled mouse models is governed primarily by the driver line used to introduce the tetracycline-controlled transactivator (tTA). Detailed maps showing where each tTA driver activates expression are therefore essential for designing and using tet-regulated models, particularly in brain research where cell type and regional specificity determine the circuits affected by conditional gene expression. We have compiled a comprehensive online repository of serial microscopic images showing brain-wide reporter expression for five commonly used tTA driver lines. We have spatially registered all images to a common three-dimensional mouse brain anatomical reference atlas for direct comparison of spatial distribution across lines. The high-resolution images and associated metadata are shared via the web page of the EU Human Brain Project. Images can be inspected using an interactive viewing tool that includes an optional overlay feature providing anatomical delineations and reference atlas coordinates. Interactive viewing is supplemented by semi-quantitative analyses of expression levels within anatomical subregions for each tTA driver line.

Pubmed ID: 30806643 RIS Download

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This is a list of tools and resources that we have found mentioned in this publication.


Neurolucida (tool)

RRID:SCR_001775

Neurolucida is advanced scientific software for brain mapping, neuron reconstruction, anatomical mapping, and morphometry. Since its debut more than 20 years ago, Neurolucida has continued to evolve and has become the worldwide gold-standard for neuron reconstruction and 3D mapping. Neurolucida has the flexibility to handle data in many formats: using live images from digital or video cameras; stored image sets from confocal microscopes, electron microscopes, and scanning tomographic sources, or through the microscope oculars using the patented LucividTM. Neurolucida controls a motorized XYZ stage for integrated navigation through tissue sections, allowing for sophisticated analysis from many fields-of-view. Neurolucidas Serial Section Manager integrates unlimited sections into a single data file, maintaining each section in aligned 3D space for full quantitative analysis. Neurolucidas neuron tracing capabilities include 3D measurement and reconstruction of branching processes. Neurolucida also features sophisticated tools for mapping delineate and map anatomical regions for detailed morphometric analyses. Neurolucida uses advanced computer-controlled microscopy techniques to obtain accurate results and speed your work. Plug-in modules are available for confocal and MRI analysis, 3D solid modeling, and virtual slide creation. The user-friendly interface gives you rapid results, allowing you to acquire data and capture the full 3D extent of neurons and brain regions. You can reconstruct neurons or create 3D serial reconstructions directly from slides or acquired images, and Neurolucida offers full microscope control for brightfield, fluorescent, and confocal microscopes. Its added compatibility with 64-bit Microsoft Vista enables reconstructions with even larger images, image stacks, and virtual slides. Adding the Solid Modeling Module allows you to rotate and view your reconstructions in real time. Neurolucida is available in two separate versions Standard and Workstation. The Standard version enables control of microscope hardware, whereas the Workstation version is used for offline analysis away from the microscope. Neurolucida provides quantitative analysis with results presented in graphical or spreadsheet format exportable to Microsoft Excel. Overall, features include: - Tracing Neurons - Anatomical Mapping - Image Processing and Analysis Features - Editing - Morphometric Analysis - Hardware Integration - Cell Analysis - Visualization Features Sponsors: Neurolucida is supported by MBF Bioscience.

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Rodent Brain WorkBench (tool)

RRID:SCR_002727

The Rodent Brain WorkBench is the portal to atlases, databases and tools developed by the Neural Systems and Graphics Computing Laboratory (NeSys) at the Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway. The Rodent Brain WorkBench presents a collection of brain mapping and atlasing oriented database applications and tools. The main category of available data is high resolution mosaic images covering complete histological sections through the rat and mouse brain. A highly structured relational database system for archiving, retrieving, viewing, and analysing microscopy and imaging data, aiming at presentation in standardized brain atlas space, is used to present a series of web applications for individual research projects. * Brain Connectivity * Atlases of Mouse Brain Promoter Gene Expression * General Brain Atlas and Navigation Systems * Downloadable tools for 3-DVisualization Open Access: * Atlas 3D * Cerebro-Cerebellar I * Cerebro-Cerebellar II * Neurotransporter Atlas * Rat Hippocampus * Tet-Off Atlas I (PrP) * Tet-Off Atlas II (PrP/CamKII) * Whole Brain Connectivity Atlas The data presented have been produced in collaboration with a large number of laboratories in Europe and the United States.

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Allen Mouse Brain Reference Atlas (tool)

RRID:SCR_002978

Allen Mouse Brain Atlas includes full color, high resolution anatomic reference atlas accompanied by systematic, hierarchically organized taxonomy of mouse brain structures. Enables interactive online exploration of atlas and to provide deeper level of 3D annotation for informatics analysis and viewing in Brain Explorer 3D viewer.

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NeuroImaging Tools and Resources Collaboratory (NITRC) (tool)

RRID:SCR_003430

Software repository for comparing structural (MRI) and functional neuroimaging (fMRI, PET, EEG, MEG) software tools and resources. NITRC collects and points to standardized information about structural or functional neuroimaging tool or resource.

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Allen Mouse Brain Connectivity Atlas (tool)

RRID:SCR_008848

Map of neural connections in mouse brain, built on an array of transgenic mice genetically engineered to target specific cell types. In addition to the connectivity data, information about the transgenic mouse lines and genetic tracers is available. Consists of high resolution 2-D projectivity image data that can be viewed side-by-side with the associated reference atlas and other reference datasets. Enables 3-D visualization and spatial/ontological search of connectivity models through a combination of manual and informatics analyses.

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Millipore (tool)

RRID:SCR_008983

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FISHER (tool)

RRID:SCR_009181

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 1st, 2022. Software application for genetic analysis of classical biometric traits like blood pressure or height that are caused by a combination of polygenic inheritance and complex environmental forces. (entry from Genetic Analysis Software)

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QuickNII (tool)

RRID:SCR_016854

Section series aligner to volumetric atlases. Software tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems.

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Zeiss Zen Lite (tool)

RRID:SCR_023747

Software tool for basic image acquisition and analysis. Zeiss ZEN microscopy software to control of axiocam microscope cameras, image transformation and measurements, image processing, image alignment for correlative microscopy, various visualization options.

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FVB/NJ (tool)

RRID:IMSR_JAX:001800

Mus musculus with name FVB/NJ from IMSR.

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C57BL/6J (tool)

RRID:IMSR_JAX:000664

Mus musculus with name C57BL/6J from IMSR.

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C57BL/6J (tool)

RRID:IMSR_JAX:000664

Mus musculus with name C57BL/6J from IMSR.

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C57BL/6J (tool)

RRID:IMSR_JAX:000664

Mus musculus with name C57BL/6J from IMSR.

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FVB/NJ (tool)

RRID:IMSR_JAX:001800

Mus musculus with name FVB/NJ from IMSR.

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FVB-Tg(Pcp2-tTA)3Horr/J (tool)

RRID:IMSR_JAX:005625

Mus musculus with name FVB-Tg(Pcp2-tTA)3Horr/J from IMSR.

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B6.Cg-Tg(Klk8-tTA)QMmay/MullMmmh (organism)

RRID:MMRRC_031780-MU

Mus musculus with name B6.Cg-Tg(Klk8-tTA)QMmay/MullMmmh from MMRRC.

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B6.Cg-Tg(Klk8-tTA)QMmay/MullMmmh (organism)

RRID:MMRRC_031780-MU

Mus musculus with name B6.Cg-Tg(Klk8-tTA)QMmay/MullMmmh from MMRRC.

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