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

Data Releases

We periodically issue new releases of our three dimensional gene expression data. Each release includes information on virtually all embryos included in all previous releases and usually information from new embryos as well. Each release is a data freeze. Metadata associated with PointCloud, VirtualEmbryo and and Correspondance files will not be changed or corrected in that release. A new release will be issued to allow access to data on new protein or mRNA patterns, data from mutant embryos, data from other Drosophila species, to correct errors in metadata, and/or when our image analysis or registration methods have improved sufficiently to generate new versions of PointClouds and VirtualEmbryos.

Current Release:
Release 2.0. Our web site allows retrieval only from our most recent data release, currently release 2. This current release contains PointCloud files from 2830 embryos which were generated using version 5.0 of our segmentation algorithms and one VirtualEmbryo and its associated Correspondence Files, and meta data. The VirtualEmbryo contains mRNA expression information from 2180 embryos summarizing data for 95 genes at six time cohorts during stage 5. It also summerizes protein expression data from 215 embryos for four proteins. It and other relevant files and information are provided on the Expression Atlas page. In addition to PointClouds used to construct the VirtualEmbryo, Release 2 contains PointClouds for stage 4 embryos and bcd, toll and dd7 mutant embryos.

Previous Releases:
Files from old data releases are provided as downloadable tar/gzip files containing PointCloud files with their associated metadata. Our previous data releases are:

Release 1.0. This contains the 1282 PointCloud files used in Luengo et al, 2006 and Keränen et al, 2006. The PointClouds in this release were made using version 4.0 of our segmentation algorithm.

Release 1.1. This contains PointCloud files from 1646 embryos, including the ones from Release 1.0, which were generated using version 5.0 of our segmentation algorithm.