10. How to define dLGN subdivisions? The distinct functional sublaminae are defined by anatomical, physiological and molecular criteria Anatomy: -- Anatomy of retinal projections --Overlapping/ Interleaving of ipsi and contra projections. -- Additional anatomic criteria Cellular organization Shapes, sizes and densities of cells (Immunostaining for neurons and glia)
11. First Analyses 1. Tracing of ipsilateral and contralateral regions in MATLAB, aligning these images for analyses. 2. Cytoarchitectonics to look for rat dLGN sub-structure in MATLAB and CellProfiler 3. Binocular region in rat dLGN? Looking for overlap
12. First Analyses 1. Tracing of ipsilateral and contralateral regions in MATLAB, aligning these images for analyses. 2. Cytoarchitectonics to look for rat dLGN sub-structure in MATLAB and CellProfiler 3. Binocular region in rat dLGN? Looking for overlap
18. Examine the brain from all angles Sagittal (contra) Coronal (contra) ?? Coronal only
19. First Analyses 1. Tracing of ipsilateral and contralateral regions in MATLAB, aligning these images for analyses. 2. Cytoarchitectonics to look for rat dLGN sub-structure in MATLAB and CellProfiler 3. Binocular region in rat dLGN? Looking for overlap
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21. 2. Cytoarchitecture with CellProfiler and Matlab – Choose the region of interest – Mask the nissl image using the geimsa outlines – Send the masked image through series of CellProfiler analyses – Look at output: Cell area, excentricity, density.
26. Cell area in different ipsilateral 'blob' projections Area pixels Slice Ipsi blob 1 Ipsi blob 2
27. First Analyses 1. Tracing of ipsilateral and contralateral regions in MATLAB, aligning these images for analyses. 2. Cytoarchitectonics to look for rat dLGN sub-structure in MATLAB and CellProfiler 3. Binocular region in rat dLGN? Looking for overlap
50. Brief Overview 1) The visual systems and the LGN 2) Why study the rat visual system? 3) Anatomy and the LGN 4) Methods: following the retinal ganglion cells to the rest of the brain. 5) Present and Future anatomical studies…
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53. How to define the Rat dLGN The distinct functional sublaminae are defined by anatomical, physiological and molecular criteria Anatomy first: -- Anatomy of retinal projections -- Additional anatomic criteria Cellular organization Shapes, sizes and densities of cells Immunostaining for neurons (NeuN) glial cells (GFAP) GABAergic interneurons (GAD) ChAT (for tectal projections). -- Interleaving of ipsi and contra projections.