One approach is to create a logical matrix for the input by comparing it to the target value. You can then sum a row, column, or the whole matrix to get the number of instances, since each instance is indicated by a 1.
% create a 50 x 50 matrix taking integers between 1 and 10
M = randi( 10 , 50 , 50 );
% the value you wish to count instances of
targetVal = 3;
% create logical matrix indicating presence of targetVal at location
isTarget = (M == targetVal);
% Find the number of instances in the matrix
nVals = sum( isTarget(:) );
% Find the number of instances in row 3
nvalsR3 = sum( isTarget(3,:) );
% Find the number of instances in column 12
nvalsC12 = sum( isTarget(:,12) );
