Z Josh Huang - US grants

The BRAIN initiative cell census network calls for large-­scale, comprehensive approaches to define the composition of the mammalian brain at the cellular level and using an overall strategy that integrates multimodal information (morphology, connectivity, molecules etc..) within a Common Coordinated Framework (CCF) to enable distribution, validation, integration and use of the atlas by the community. The BICCN challenge is enormous and remains a scientific problem requiring new discovery, continuous innovation in methods, technologies and pipeline of analysis. Given the unparalleled cellular diversity of the mouse brain and the need for an informed cell classification scheme, we propose here an ambitious project that addresses both the need for scale (coverage of millions of cells) and depth of analysis of each cell and, further, that integrates molecular and anatomical information. To address this challenge, we have assembled a collaborative group of key knowledge leaders and innovators across various fields of neuroscience, genomics, and technology. First, we will apply transformative new droplet scRNA sequencing technologies and next-­generation computational methods and data processing pipelines to compile a whole brain cell transcriptome atlas on a massive scale (millions of single cells and nuclei collected brainwide). This effort will generate an unprecedented inventory of cell type composition and distribution for the mouse brain within the CCF. Second, we will generate a forebrain neuronal atlas that will integrate detailed molecular information (to saturation) of anatomically defined populations with high-­resolution morphological and connectivity information to provide an in-­depth picture of a core portion of the mammalian brain. We will also generate highly specific driver lines for precise marking of cell types and to enable adaptive methods that refine cell sampling to achieve completeness. Finally, realizing the need for innovation in technology to enable work that is made difficult because it requires both scale and precision, we will devote key effort to develop new integrated technological platforms that combine multiple methods to relate neuronal connectivity with transcriptomes and cellular distribution at an unprecedented scale. Our Data Core will integrate, store, and manage multi-­modal datasets and provide bioinformatics and computational expertise;? and our Administrative Core, will coordinate and oversee Center-­wide activities. Our effort is unprecedented for scale and coverage, and it relies on a team of investigators with demonstrated academic track records of innovation in technology and neurobiology, working in an environment that allows for implementation of massive pipelines for production workflow. This will guarantee progressive evolution and innovation of methods, experimental design and analysis to meet future challenges and succeed at generating a comprehensive molecular and anatomical atlas of the mouse brain.

ANATOMY RESEARCH SEGMENT SUMMARY   The  overarching  goal  of  neuroanatomy  is  to  establish  a  structural  framework  to  integrate  multiscale  and  multi-­modal information and to provide a road map that guides the exploration of neural dynamics and brain  function.  ?Anatomic?  neuron  types  can  be  described  by  their  location,  morphology,  and  connectivity.  As  morphology is one of the most intuitive depictions of cell types that reflects their input-­output connectivity, the  visualization,  characterization  and  quantification  of  their  complete  and  detailed  shapes  are  key  to  the  identification  and  classification  of  anatomic  neuron  types.  However,  these  have  remained  enduring  challenges for over a century, as most vertebrate neurons are simultaneously small and large, spanning vast  spatial scales from submicron to centimeter (e.g. corticospinal neurons connecting cortex to spinal cord). The  overall goals of the Anatomy Segment are to: 1) establish a Forebrain Projection Cell Atlas that integrates  in-­depth multi-­modality anatomic and molecular information across cerebral cortex, basal ganglia, thalamus,  and  hypothalamus.  A  forebrain  projection  neuron  atlas  will  provide  a  core  skeleton  that  anchors  nearly  all  other  brain  structures  and  the  transcriptome  cell  atlas  constructed  in  the  Molecular  Segment;?  2)  advance  current  and  emerging  imaging  technologies  and  pipelines  with  improved  resolution,  throughput  and  lower  cost.  We  will  use  several  state-­of-­the-­art  imaging  technologies  and  pipelines  to  obtain  multi-­modal,  high-­ resolution  whole  brain  datasets  on  cell  location,  morphology,  projection,  and  connectivity  of  vast  sets  of  forebrain  neurons,  all  registered  in  the  mouse  brain  Common  Coordinate  Framework  (CCF).  To  achieve  high-­resolution  brain-­wide  imaging,  we  will  use  1)  Serial  Two-­Photon  tomography  (STP)  to  image  marker-­ defined  neuronal  body  distribution,  2)  STP  to  image  axon  projection  patterns  of  genetic  and  virally-­labeled  neuron  subpopulations,  3)  fluorescence  Micro-­Optical  Sectioning  Tomography  (fMOST)  to  image  and  reconstruct  the  complete  morphology  of  single  neurons  ?  the  ultimate  resolution  for  anatomic  cell  typing.  Importantly,  this  anatomical  forebrain  atlas  will  integrate  single-­cell  molecular  information  collected  and  positionally  mapped  for  the  same  cell  types  in  the  Molecular  Segment,  towards  a  close-­to-­completion  Molecular and Anatomical atlas of the mouse forebrain.   

OVERALL SUMMARY   The  BRAIN  initiative  cell  census  network  calls  for  large-­scale,  comprehensive  approaches  to  define  the  composition of the mammalian brain at the cellular level and using an overall strategy that integrates multimodal  information  (morphology,  connectivity,  molecules  etc..)  within  a  Common  Coordinated  Framework  (CCF)  to  enable  distribution,  validation,  integration  and  use  of  the  atlas  by  the  community.  The  BICCN  challenge  is  enormous and remains a scientific problem requiring new discovery, continuous innovation in methods,  technologies and pipeline of analysis. Given the unparalleled cellular diversity of the mouse brain and the  need for an informed cell classification scheme, we propose here an ambitious project that addresses both the  need  for  scale  (coverage  of  millions  of  cells)  and  depth  of  analysis  of  each  cell  and,  further,  that  integrates  molecular and anatomical information. To address this challenge, we have assembled a collaborative group of  key knowledge leaders and innovators across various fields of neuroscience, genomics, and technology. First,  we  will  apply  transformative  new  droplet  scRNA  sequencing  technologies  and  next-­generation  computational  methods and data processing pipelines to compile a whole brain cell transcriptome atlas on a massive scale  (millions of single cells and nuclei collected brainwide). This effort will generate an unprecedented inventory of  cell type composition and distribution for the mouse brain within the CCF. Second, we will generate a forebrain  neuronal  atlas  that  will  integrate  detailed  molecular  information  (to  saturation)  of  anatomically  defined  populations with high-­resolution morphological and connectivity information to provide an in-­depth picture of a  core portion of the mammalian brain. We will also generate highly specific driver lines for precise marking of cell  types and to enable adaptive methods that refine cell sampling to achieve completeness. Finally, realizing the  need  for  innovation  in  technology  to  enable  work  that  is  made  difficult  because  it  requires  both  scale  and  precision,  we  will  devote  key  effort  to  develop  new  integrated  technological  platforms  that  combine  multiple  methods to relate neuronal connectivity with transcriptomes and cellular distribution at an unprecedented scale.  Our  Data  Core  will  integrate,  store,  and  manage  multi-­modal  datasets  and  provide  bioinformatics  and  computational expertise;? and our Administrative Core, will coordinate and oversee Center-­wide activities. Our  effort  is  unprecedented  for  scale  and  coverage,  and  it  relies  on  a  team  of  investigators  with  demonstrated  academic track records of innovation in technology and neurobiology, working in an environment that allows for  implementation  of  massive  pipelines  for  production  workflow.  This  will  guarantee  progressive  evolution  and  innovation of methods, experimental design and analysis to meet future challenges and succeed at generating  a comprehensive molecular and anatomical atlas of the mouse brain.