3D Gene Expression

Expression Atlases
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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

Correspondence File Format

Correspondence files are text files with a '.cor' extension and contain the correspondence computed between an individual PointCloud and a morphological template while building a gene expression atlas. The syntax is similar to that of individual PointCloud files.

This file format is compatible with the 'comma-separated values' (.csv) format, and should be readable in applications such as Excel. Meta-data is written to a header in lines starting with a '#' character. These lines conform to a certain syntax specified below. Lines starting with a double '##' are comments. The actual comma-separated values form a table in which each row contains data for a single nucleus with entries specifying the correspondences.

Each row has the form:

id,n,id_1,id_2,...id_n,wt_1,wt_2,...,wt_n
The first entry in each row specifies the ID of a nucleus in the morphological template which can be found in the VirtualEmbryo file associated with an atlas. The second entry in each row specifies the number of corresponding nuclei in the source PointCloud. This is followed by a list of source nuclei ids and then a list of weights. Weights are used in computing the average in the VirtualEmbryo. A typical row with exactly one source nucleus might look like:
8,1,1302,1.00

Meta-data lines are of the form:

   # key = value

where key is the name of a property, and value can be either a number, a string or an array of numbers or strings. A value can also be empty. A string is distinguished from a number by enclosing it in double-quotes ("). An array is enclosed in square brackets ([]), with the elements in a row separated by commas and the rows separated by semi-colons (see examples below).


These are the property names currently used in the Correspondence file:

src_name (string)
The name of the source PointCloud for which this correspondence was computed.
src_nuclearcount (integer)
Number of nuclei in the source PointCloud.
dst_name (string)
The name of the destination atlas for which this correspondence was computed.
dst_nuclearcount (integer)
Number of nuclei in the destination morphological template.
total_displacement (float)
The total average displacement for the given mapping of source nuclei to destination nuclei locations.
distortion_cost (float)
Cost of the distortion associated with the warping of source onto target.
matching_failed (boolean)
Flagged as 1 if the matching procedure failed for some reason (e.g. missing marker gene, overly large distortion cost, too many outliers, etc)

Sample excerpts from a Correpsondence file