Supplementary Video 1 | Computation of an average brain nuclear stain intensity. Overlay of the nuclear stain data for all 71 larvae in the database. The average nucleus channel was computed from all larvae in the database. The movie shows the stack from dorsal to ventral. Download: video_01_average_brain.avi (9.5M) | video_01_average_brain.m4v (377K)
Supplementary Video 2 | Grouped anatomical segmentation of reference larva 3D volume. Surface rendering of each anatomical part, grouped by major brain regions, in movie sequence. Dorsoanterior view; for color code see Supplementary Table 2. (Download high resolution video_02_grouped_anatomical_segments.avi)
Supplementary Video 3 | Individual anatomical segmentation of reference larva 3D volume. Surface rendering of each anatomical part individually in a movie sequence. Dorsoanterior view; for color code see Supplementary Table 2. (Download high resolution video_03_individual_anatomical_segments.avi)
Supplementary Video 4 | Anatomical segmentation of reference larva 3D volume with color-coded anatomical regions. For color code, see Supplementary Table 2. The movie shows the stack from dorsal to ventral. (Download high resolution video_04_full_segmentation_regions_and_mask.avi)
Supplementary Video 5 | Anti-TH immunofluorescence combination of data stacks with the anatomical model in white lines. This representation identifies anatomical domains of gene expression stain of e138, e139 and e141 combined into anatomical standard model. The movie shows the stack from dorsal to ventral. The intensities have been assigned the ImageJ Fire-LUT colors (color code: see Figure 4b). The data stacks are combined with the anatomical model segment borders in white lines to identify anatomical domains of gene expression. (Download high resolution video_05_TH_segmented_white_line.avi)
Supplementary Video 6 | Anti-TH immunofluorescence combination of data stacks with the anatomical model in color representation. This representation identifies anatomical domains of gene expression stain of e138, e139 and e141 combined into anatomical standard model. The movie shows the stack from dorsal to ventral. The intensities have been assigned the ImageJ Fire-LUT colors (color code: see Figure 4b). The data stacks are combined with the anatomical model in color, for color code see Supplementary Table 2. (Download high resolution video_06_TH_segmented_color_regions.avi)
Supplementary Video 7 | TH and Vmat2 colocalization. Colocalization analysis of TH (green, anti-TH immunofluorescence, three-larva overlay) and Vmat2 (red, anti-GFP immunofluorescence in vmat2:GFP, three-larva overlay) revealing colocalization of TH and Vmat2 expression in catecholaminergic neurons. The movie shows the stack from dorsal to ventral. (Download high resolution video_07_TH_vmat2_colocalization.avi)
Supplementary Video 8 | TH, Vmat2, and Otpb colocalization. Colocalization analysis of TH (red, anti-TH immunofluorescence, three-larvae overlay), Vmat2 (blue, anti-GFP immunofluorescence in vmat2:GFP, three-larva overlay) and Otpb (green, anti-GFP immunofluorescence in otpb:GFP, three-larva overlay) revealing colocalization of TH, Vmat2 and Otpb expression in posterior tubercular dopaminergic neurons. The movie shows the stack from dorsal to ventral. (Download high resolution video_08_TH_vmat2_otpb_colocalization.avi)
Supplementary Video 9 | TH, AcTub, and 3A10 colocalization. Analysis of axon bundles containing acetylated tubulin (blue, anti-AcTub immunofluorescence, three-larva overlay), TH (red, anti-TH immunofluorescence, three-larva overlay) and surface antigen 3A10 (green, 3A10 immunofluorescence in otpb:GFP, three-larva overlay). The movie shows the stack from dorsal to ventral. (Download high resolution video_09_TH_AcTub_3A10_colocalization.avi)
Supplementary Video 10 | Dlx5a/6a, Foxd3 and Emx3 colocalization. Analysis of the relative positioning of the expression domains of transcription factors involved in brain patterning and differentiation: Dlx5a/6a domain (blue, anti-GFP immunofluorescence in dlx5a/6a:GFP, three-larva overlay), Foxd3 (red, anti-GFP immunofluorescence in foxd3:GFP, three-larva overlay) and Emx3 (green, anti-GFP immunofluorescence in emx3:GFP, three-larva overlay), revealing exclusion expression domains and localization of boundaries between domains. The movie shows the stack from dorsal to ventral. (Download high resolution video_10_dlx5a6a_foxd3_emx3_colocalization.avi)
Supplementary Video 11 | Multi-expression analysis. Virtual qualitative colocalization analysis of 11 different expression patterns representing 33 stained larvae. The color code is shown in Figure 4i. The movie shows the stack from dorsal to ventral. (Download high resolution video_11_multi_expression.avi, or raw data as tiff stack for ImageJ: video_11_multi_expression_rawdata.tif (573MB))
Supplementary Video 12 | Protein and mRNA signal colocalization. Registration of tyrosine hydroxylase mRNA (th WISH, red; three larvae) and protein (anti-TH immunofluorescence, green; three larvae) detection reveals colocalization of catecholaminergic somata. The movie shows a stack from dorsal to ventral. (Download high resolution video_12_protein_and_mRNA_colocalization.avi)
Supplementary Video 13 | WISH data registration. Registration of Tbr1b transcription factor (green, WISH, three larvae) and Glyt2 marker for glycinergic neuron (red, WISH, three larvae) mRNA expression to the anatomical model (blue lines). In this stack the nuclear stain calculated for the 3-dpf average larvae is shown for reference. The movie shows a stack from dorsal to ventral. (Download high resolution video_13_WISH_data_registration.avi)