http://confocal-microscopy-list.275.s1.nabble.com/What-has-happened-to-extended-focus-in-Leica-Software-tp4427300p4435870.html
So Carl's concern was correct, this is redefining the term. If one does not have access to the Leica software, ImageJ can do this through the 3D Project... command (requires 8-bit or RGB). select projection method and choose Z-Axis for axis of rotation. Set Total Rotation = 0 and enter your desired Lower and Upper Transparency Bounds to set the threshold. Look at the ImageJ documentation for using the depth cueing and opacity settings.
> Torsten
>
> The TCS NT implementation of extended focus is a direct average of each column with the result resampled back to 8-bit. In the newer LAS implementation Leica have added a threshold feature so you can calculate an average projection without including the dark/black pixels which tend to dilute detail in parts of the sample surrounded above and below by dark pixels/voxels. The end result is a projection intermediate between average intensity and maximum intensity which is why your new images look different. I usually simplistically explain to users that maximum intensity tends to find surfaces while extended focus gives a more transparent rendering.
> If you are using LAS you should be able to get a projection the same as the old software if you set the threshold to 0.
>
> Dr Lloyd Donaldson
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> From: Confocal Microscopy List [mailto:
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> Sent: Saturday, 23 January 2010 1:59 a.m.
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> Subject: Re: What has happened to "extended focus" in Leica Software?
>
> 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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