Re: What has happened to "extended focus" in Leica Software?

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URL: http://confocal-microscopy-list.275.s1.nabble.com/What-has-happened-to-extended-focus-in-Leica-Software-tp4427300p4433726.html

Assuming you do a simple top down projection then a maximum or average project will just consider a single pixel/voxel per Z section in the calculation. You would use them as Guy Cox suggests, maximum is the default and easy 1 click mode as it usually looks fine. If you took your Z-stack ok then max brightness is idiot proof. Average is better for almost saturated images.

The name extended focus implies a slightly more complex algorithm than just analysing a single voxel per plane. These algorithms will look for which Z plane has the ‘best’ information, meaning most in focus information. This is usually determined by looking at regions within each plane and looking for the local energy. The section with the highest energy for that region is selected. Unlike average and maximum brightness projections extended depth tend to vary in implementation between software programs I have seen as there are different algorithms like High-pass for picking what is in focus.

Extended focus algorithms are traditionally best for transmitted light images where the inverted contrast makes techniques like max brightness and average not suitable.

I would just ask what the replacement for this previous Extended focus is and what they recommend for the transmission source is.

Regards
 - Martin

On Thu, Jan 21, 2010 at 2:39 PM, Robert J. Palmer Jr. <[hidden email]> wrote:

Torsten - I meant ask Leica about the algorithm, which does not belong to the two "simple" ways to do a projection (maximum or average).

Thanks everyone for the replies!

Guy - I did the deconvolution on the whole stack, not the projection... ;-)

But I still don't know what kind of algorithm Leica used for the "Extended Focus" function in the old software package. Today I took my old .tif stacks and produced new projections (maximum and average) with the Leica LAS package, but they don't look as the old pictures I still have on my hard disk (from the old equipment)... So I get three different projection versions from a single stack.

Robert - I contacted Leica to get another licence key, as it is depends on a hardware key the setup program of the TCS NT PowerScan software produces...  (I try to install the old package on a modern PC; Win NT works fine so far). Actually, I send the first email to the list b/c I am almost always surprised about the responses... Over the years I learned a lot from the list...:-)

Glen - Thanks for this hint, I will give the ImageJ plugin a try asap!

:-)  Torsten

 

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