pad_and_find_candidate_somata.m

function feature_struct_from_candidate_index = ...
    pad_and_find_candidate_somata(rendered_folder_path, ...
                                  gfp_channel_index, ...
                                  background_channel_index, ...
                                  zoom_level, ...
                                  origin_at_zoom_level_xyz, ...
                                  spacing_at_zoom_level_xyz, ...
                                  substack_origin_ijk1, ...
                                  substack_shape_ijk, ...
                                  pad_depth_in_um, ...
                                  parameters)
    % substack_origin_ijk1 is the origin of the substack within the full stack at this zoom

    substack_shape_xyz = spacing_at_zoom_level_xyz .* substack_shape_ijk ;
    substack_origin_xyz = origin_at_zoom_level_xyz + spacing_at_zoom_level_xyz .* (substack_origin_ijk1-1) ;

    pad_depth_ijk = ceil(pad_depth_in_um ./ spacing_at_zoom_level_xyz) ;  % 3 x 1
    padded_substack_origin_ijk1 = substack_origin_ijk1 - pad_depth_ijk ;
    padded_substack_shape_ijk = substack_shape_ijk + 2*pad_depth_ijk ;
    
    padded_substack_yxz = ...
        get_mouselight_rendered_substack(rendered_folder_path, gfp_channel_index, padded_substack_origin_ijk1, padded_substack_shape_ijk, zoom_level) ;  
    padded_background_substack_yxz = ...
        get_mouselight_rendered_substack(rendered_folder_path, background_channel_index, padded_substack_origin_ijk1, padded_substack_shape_ijk, zoom_level) ;  

%     substack_mip = max(padded_substack_yxz,[], 3) ;
% 
%     figure('color', 'w') ;
%     imagesc(substack_mip) ;
%     colormap(gray(256)) ;
%     axis image

    padded_substack_origin_xyz = spacing_at_zoom_level_xyz .* (padded_substack_origin_ijk1-1) + origin_at_zoom_level_xyz ;  
        % coord of voxel center of lowest-indices voxel

    feature_struct_from_candidate_index = ...
        find_candidate_somata_in_uint16_stack(padded_substack_yxz, ...
                                              padded_background_substack_yxz, ...
                                              padded_substack_origin_xyz, ...
                                              origin_at_zoom_level_xyz, ...
                                              spacing_at_zoom_level_xyz, ...
                                              substack_origin_xyz, ...
                                              substack_shape_xyz, ...
                                              parameters) ;
        
%   find_candidate_somata_in_uint16_stack(padded_substack_yxz, ...
%                                               padded_substack_origin_xyz, ...
%                                               origin_at_zoom_level_xyz, ...
%                                               spacing_at_zoom_level_xyz, ...
%                                               substack_origin_xyz, ...
%                                               substack_shape_xyz, ...
%                                               parameters)        
        
end