Thanks for your question. There are several applications that use AGEA tools, or Anatomical Gene Expression Atlas data analysis for viewing relative abundance of transcripts based on in situ hybridization image data. It’s not clear which application you are referring to, but your question can be generalized to multiple applications, and it seems like you are already familiar with some documentation. A Help section provides general information, and more information is in the detailed user guide and corresponding publication by Ng, et al. (2009). https://www.nature.com/articles/nn.2281
As an example, consider the Adult Mouse AGEA application here. Regarding ‘fold change’ and sample sizes, recall that the visualization presents an average rendering based on data from many images and multiple experimental sources that are mapped into a ‘voxel’ space; there is not a specific ‘sample’ referenced as a source. The ‘crosshairs’ reflect a seed position from which a Pearson’s coefficient is calculated at a voxel (which is 200 um3), so a specific specimen-area is not defined using this visualization tool - it’s a spatial coordinate. This should be more clear if you read through the detailed documentation, where the correlation is the critical consideration, not ‘fold change.’ Fold change is provided as a relative measure, referring to the gene expression intensity in the selected voxel over the thresholded voxels. The ‘gene list’ is a ranked list of experiments based on voxel-mapped quantification of image data correlating with the seed selected target voxel (crosshair intersection).
To learn more about the processing for the Developing Mouse application, you can launch a help page from the Documentation tab on the main data access page, with detailed information in Technical Whitepapers, in Informatics Data Processing (a downloadable PDF document; refer to page 7).
Hopefully this helps!