Additional file 1: Movie S1. Fluorescence (FM-AT) and electron (EM-AT) images of a single mouse cortex array section, overlaid in pixel-precise register illustrating combination of multichannel FM of a large area (approximately 0.4 × 1.0 mm, spanning all six cortical layers) with EM sampling of a smaller subfield (unpublished Allen Institute data). (Procedures as schematized in arrow track 3, Fig. 2. The rationale for registering a large FM-AT field with a much smaller EM-AT field is discussed in the text section “What limits AT specimen size”). In this video rendering, the field of view gradually zooms 200-fold into a very small subfield in layer 5. At the higher zooms, it is evident that synaptic protein (PSD95, GluN1, VGluT1, Synapsin, GAD2 and Gephyrin), nuclear DNA (DAPI), myelin (MBP), and GABA markers align with EM images as expected from current biological models of mammalian cortex and synapses. Colors representing ten channels of molecular fluorescence are modulated periodically in this video to better accommodate the limitation of human color vision to (at most) three discrete color channels. The specimen samples VISp cortex of a transgenic mouse in which expression of a fluorescent protein (TdTomato) was driven mainly in layer 4 pyramidal cells [103] (MOV 117816 kb)
Download video file (115.1MB, mov)