C. elegans with its precise cell lineage and limited number of cells is predestined for the study of genes and developmental events at the level of single cells. Ultimately, one would want to know the precise spacio-temporal profile at the RNA and protein level of the thousands of molecules involved in controlling developmental decisions, which would then allow mathematical modeling. To obtain live GFP recordings through embryogenesis we developed a 2-channel 4D recording Automation in Openlab. We choose to use the DIC channel for lineaging and cell identification purposes, since DIC microscopes are most commonly available in the C. elegans field. We have empirically determined conditions that allow us to record through embryogenesis using a digital camera without affecting viability. We are successfully recording embryonic expression patterns for homeobox genes, such as ceh-36, ceh-37, ceh-20, ceh-5, ceh-33, ceh-34, ceh-41, etc. (see abstract by A. Abouzied). These analyses have revealed unexpected dynamic early expression patterns. Ultimately the 4D expression data need to be converted into a digital form. This prompted us to develop 'Virtual Worm'-Base (VW-Base), an interactive 4-dimensional C. elegans database. In its first iteration, C. elegans is represented as a 3-D model based on the positions of the nuclei that can be rotated and viewed through time, but includes also standard lineage windows. The 4D worm model has all the features to identify, highlight, and label cells to make it a useful tool cell visualization and instruction purposes. 4D microscope recordings are imported into VW-Base for lineage and cell identification purposes. Once cells are identified, the identity of the GFP positive cells is also known and VW-Base is used as a tool to enter the expression data by clicking on the positive cells. Such expression data is then exported in a digital format that hopefully can be deposited with an accession number at Wormbase. This reduces the need for second hand data entry for Wormbase curators. C. elegans researchers can download deposited expression data and view and search them in any combination in VW-Base. The goal is to make VW-Base as flexible as possible by allowing different data formats, and different lineage channels (e.g. GFP-histone instead of DIC) so that as many people in the field can use it and contribute expression patterns, be it GFP, RFP or antibody data. We plan to improve the lineaging features by adding automatic routines. The ultimate goal would be to have completely automatic lineaging and automatic expression detection. Other ideas would be to have cell outlines as 3D models, and to include neuronal network data.

Affiliation:
- Karolinska Institutet, Sdertrns Hgskola, SWEDEN