DOI: 10.5061/dryad.4xgxd2593
title: The cell adhesion molecule Sdk1 shapes assembly of a retinal circuit that detects localized edges

description: Nearly 50 different mouse retinal ganglion cell (RGC) types sample the
 visual scene for distinct features. RGC feature selectivity arises from
 its synapses with a specific subset of amacrine (AC) and bipolar cell (BC)
 types, but how RGC dendrites arborize and collect input from these
 specific subsets remains poorly understood. Here we examine the hypothesis
 that RGCs employ molecular recognition systems to meet this challenge. By
 combining calcium imaging and type-specific histological stains we define
 a family of circuits that express the recognition molecule Sidekick 1
 (Sdk1) which include a novel RGC type (S1-RGC) that responds to local
 edges. Genetic and physiological studies revealed that Sdk1 loss
 selectively disrupts S1-RGC visual responses which result from a loss of
 excitatory and inhibitory inputs and selective dendritic deficits on this
 neuron. We conclude that Sdk1 shapes dendrite growth and wiring to help
 S1-RGCs become feature selective.
description: Two Datasets are provided. 1) Sample
 registration data - contains images, code, and ROIs to register two-photon
 imaged fields of retinae containing GCaMP6f+ RGCs with the same retinae
 following staining with antibodies to marker genes for Sdk1 RGC
 types. 2) Visual response data - contains responses of
 Sdk1 RGCs to a full-field flash and moving bar, grouped according to
 expression of Ost, Brn3c, Nr2f2, and Calbindin.
description: <strong>1) Sample registration
 data.</strong> Stitch2p is a function that registeres 2p
 and 1p images of retina. INPUT: 
 PATH: is the string path where the recordings are
 saved. RANGE is a 1x2 matrix that defines the range
 of movies to include in the analysis this works because each recording is
 assigned a number matching their order(movie_n). eg: calling [0 3] will
 analyze movie_0 to movie_3 in the specified path.
 CENTER is a path containing the blood vessel pattern acquired
 during the recording session. 
 OUTPUT: ROIS =  struct with all
 the 2p recording movies and bloodvessels used in the stiching
 STITCHED: Array with raw stitched image
 TESTIMAGE: converted 8bit image with color multiplier for
 visualization to use with provided sample images open
 matlab and set the path and center variables. 
 For example: path =
 "C:\Downloads\Remapping process files\sample 2p
 recordings" center =
 "C:\Downloads\Remapping process files\sample 2p
 recordings\movie_10" Stich2p(path,[0
 3],center); Should display a stitched
 image and save it, along with a matfile, to the path defined in
 'center' Example images: any folder in the
 "sample 2p recordings" folder will contain example files of
 remapped images along with original recording<br> data. Remapped
 images are based on the image in the "confocal ROIs"
 folder. File naming definitions: 
 RoiSet: mask containing the cells of
 interest. bloodvessels: mask
 containing the bloodvessels for marker intensity calculations
 stim_x: individual presented stimuli along
 with relevant information 
 expression_23_06_20_mx: CSV file containing assigned
 markers remap: the remapped image
 from which the markers where assigned 
 remap_points: land mark points used to make the
 Remapped image landmark points are listed as the confocal and 2p
 image. <strong>2) Visual
 response data:</strong> Matfile (*.mat)
 containing a single struct called 'compiled'.
 Struct field definitions: mb:
 struct containing rawTrace: Response averaged from 2
 presentations of a bar moving in 8 different directions. Bar velocity =
 1000um/sec. 8-bar sequence was preceded by a brief (.5s) flash.
 stimTrace: vector showing stimulus timing
 allignedTrace: Time x bar array with RGC responses corrected for
 position mbAngleOrder: bar direction
 vcctor rawTime: time vector for rawTrace
 allignedTime: time vector for allignedTrace
 ff: struct containing 
 rawTrace: response averaged from 3 presentations of a full field
 flash. rawtime: time vector for rawTrace
 stimTrace: vector showing stimulus timing 
 mbs: struct ordered the same way as mb. Contains
 data averaged from 2 presentations of a bar moving in 8 different
 directions. Bar velocity = 200um/sec. 8-bar sequence was preceded by a
 brief (.5s) flash. ROI: struct containing:
 mask - binary mask that
 defines RGC. xy:
 Roi centroid position. ost, Brn3c, nr2, calb, gfp: 8bit
 intensity of the indicated marker within RGC ROI defined by
 mask. size: Roi
 area. mrk: Marker classification.
 theta: angular preference computed from moving bar stimulus and
 set relative to retinal orientation. dsi: direction
 selective index computed from moving bar stimulus.
 osi: orientation selective index computed from moving bar
 stimulus.