Issue while trying to use imopen

Hello Everyone,

I have a segmentation volume created after processing an image stack by pixel classification.

However, the presence of tiny sharp endpoints (circled black in the image here) creates an issue while trying to extract the centerline lengths.

So I tried to remove these small, sharp endpoints by performing an erosion followed by dialtion (imopen) before reconstructing of the 3D volume.

input.tiff is the input file

vessels_seg = loadtiff('input.tiff');
num_slices = size(vessels_seg);
vessel_seg_bin = vessels_seg==1;
se_open = strel('sphere',2);
vessel_seg_open = imopen(vessel_seg_bin,se_open);

post_vessels = vessel_seg_open>0;

vessels_processed_name = strcat(shortfile,'_post_processed.tif');
num_slices = size(vessels_seg,3);

 imwrite(uint8(vessels_processed(:,:,1)),vessels_processed_name);
         
    for p = 2:num_slices
            imwrite(uint8(vessels_processed(:,:,p)),vessels_processed_name, 'WriteMode','append');
    end   

end

Unfortunately, this returns a stack with all black pixels. Could someone please look into this?

Please note: loadtiff used for loading multipage tiff can be found here