The LOSSST algorithm

• LOSSST - the LOcal Spatial Similarity Search Tool is used to retrieve examples of gene expression patterns with regions of local spatial similarity to any query region.
• The query domain is either defined by a user by 'painting' on a view of one of the EMAP virtual embryo models, or if using the 'Find Similar Expression Patterns' icon: , is the mapped expression pattern domains corresponding to an EMAGE database entry.
• Wholemount searches can be restricted to either the left or right hand side of the embryo - the default is to search both the left and right sides.
• Some pairs of WM virtual embryos at adjacent stages of development have had anchor points added, which denote roughly similar anatomical points at the two stages. This allows spatial transformation of data across two or more stages of development (currently between TS15 and TS19). The available stage range for data query from each model is indicated in the LOSSST interface.

An example query:

The underlying mechanism:

The query region is defined by a user on an EMAP virtual embryo model (in this case TS11 - shown in magenta). The LOSSST algorithm initially dilates 30 pixels (or voxels for 3D queries) from the edge of the user defined region to define a local comparison region on the virtual embryo model (indicated by the dashed line). All spatial annotations for EMAGE database entries that have been annotated to the same model are then spatially compared to the query region using the Jaccard Index, but only within the local comparison region. Jaccard Index similarity coefficient scores are calculated using Woolz functions. A Jaccard Index similarity coefficient score of 1 indicates exact spatial similaity between the query region and the mapped pattern. Progressively smaller Jaccard Index similarity coefficient scores indicate patterns that are progressively less spatially similar. Note that for the purpose of simplicity, this example only displays the 9 most similar patterns out of 50+ patterns that intersect with the query region, and does not show the least spatially similar 40+ patterns.