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Standard Anatomical and Visual Space for the Mouse Retina: Computational Reconstruction and Transformation of Flattened Retinae with the Retistruct Package

Figure 5

Measurement of the ipsilateral projection. A,

Schematic illustrating the retinal label resulting from bilateral injections of Fluoro-Ruby (magenta) and Fluoro-Emerald (cyan) dye into the dLGN. B, Flat-mounted retina with label resulting from bilateral injections of Fluoro-Ruby (magenta) and Fluoro-Emerald (cyan) into left and right dLGN, respectively. C–D, Azimuthal equilateral projection of reconstructed retina in B. Isodensity contours for 5%, 25%, 50%, 75% & 95% are plotted using the kernel density estimates (KDEs) for fully sampled retinae (C) or kernel regression (KR) estimates for partially sampled retinae (D). Blue diamond is the peak density and magenta (C) or cyan (D) diamond is the Karcher mean. Yellow circle is the optic disc. E, Composite plot with ipsilateral label from unilateral injections (). Black dashed lines represent the median angle from the optic axis to the peripheral edges of the 5% isodensity contour. Coloured diamonds represent the Karcher means of the label in the individual retinae and large coloured circles are the optic discs for the individual retinae. White square and circle represent the average Karcher mean. The central dashed angle represents the median central edge of the 5% isodensity contour. F, Mean distances from either optic disc or optic axis of reconstructed retinae to the central edge of the 5% isodensity contour along a line passing through the Karcher mean of the label. G, The extent of the ipsilateral label and the distance beyond the horizontal and vertical axes. Grid spacing is 20°. In F–G, line represents the mean and error bars are standard error of the mean. Scale bar in C & D is 1 mm.

Figure 5

doi: https://doi.org/10.1371/journal.pcbi.1002921.g005