Remove noise from OCT

can you help me choose the corrected plugin for remove noise from OCT macula enhanced depth imaging like this IbrahimM_001

Hello Manar -

You might start with some of the noise-reduction filters that ship
with Fiji / ImageJ. Note, noise-reduction filters, in general, will tend
to blur your image somewhat. The Kuwahara filter is designed to
preserve edges to some extent.

Here is the result of running
Process > Filters > Kuwahara Filter
(with “Sampling window width” of 7):

oct_kuwa_7

And here is result of running
Process > Noise > ROF Denoise
(with “Theta” of 50) after the Kuwahara filter (and converting to
32-bit grayscale):

oct_kuwa_7_rof_50

Notice that in both cases the “200 μm” legend in the lower left corner
is degraded, and is almost entirely blurred out in the second version.
That’s typical of the information loss caused by noise reduction.

Perhaps this will give some ideas to start with. (There are a lot
of other noise-reduction-filter plug-ins that don’t ship out of the
box with Fiji that might also be worthwhile.)

To my eye, the second (filtered with both the Kuwahara and ROF
filters) looks a little better – but a little blurrier. But it really depends
on your particular use case and what information you need to
preserve.

Thanks, mm

1 Like