3D Gene Expression

Expression Atlases
Search PointClouds
Browse PointClouds
Data Releases

Overview:
   Summary
   Project Goals

Methods:
   Staining & Mounting
   Probe Constructs
   Staging
   Imaging

Software:
   PointCloudXplore
   PointCloudToolBox
   PointCloudAlign
   NODE

File Formats:
   PointCloud (.pce)
   VirtualEmbryo (.vpc)
   Correspondence files

 Software Download:
       PointCloudAlign-1.0
 User Guides:
      VirtualEmbryo File Format
      Correspondence File Format

Registration Methods: PointCloudAlign

Each PointCloud gives a snapshot of spatial expression levels for two or three gene products in a given embryo at a given developmental time point. To meaningfully analyze expression data from multiple PointClouds it is necessary to identify homologous nuclei in different embryos. This is made difficult due to variations in blastoderm shape and size and the lack of distinctive morphological keypoints.

PointCloudAlign utilizes a registration marker gene (typically ftz or eve mRNA patterns) in order to align each PointCloud with a standard morphological template. Once a set of PointClouds have been aligned with the model, expression measurements can be transferred onto the template to yield a VirtualEmbryo that may include aligned expression patterns for 10s or 100s of genes (Fowlkes et al, 2008). VirtualEmbryo expression data is stored in essentially the same file format as individual PointCloud, described here, and can be easily visualized with PointCloudXplore.