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Imaging Notes for Female Reference Brain:

Confocal images were taken on a Zeiss Inverted LSM 880 laser scanning confocal with a 25X/0.8NA immersion corrected objective.

Glycerol was used as the immersion medium to most closely match the refractive index on Vectashield.

The reference brain was generated with 1μm voxels as a tiled scan with 10% overlap. Blind deconvolution was performed with AutoquantX3 software.

In order to use ClearMap to warp brains to this standard brain, all images must be taken with 1μm square voxels or down sampled to this resolution.


Analysis Pipeline

The female Ae. aegypti reference brain was immunostained to label the synaptic protein Brp and imaged using confocal microscopy, as described above. The images were subjected to blind deconvolution to increase resolution. The female brain was manually annotated using the segmentation and 3D reconstruction software ITK-SNAP. This data is available to browse in our Brain Browser, and was also exported for viewing using the data analysis and visualization software ParaView. The reference brain is used as a template for brain registration using the python program ClearMap. This application is being used to examine the expression patterns of newly generated driver lines in Ae. aegypti.