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

Posted by Lloyd Donaldson on
URL: http://confocal-microscopy-list.275.s1.nabble.com/What-has-happened-to-extended-focus-in-Leica-Software-tp4427300p4435764.html

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

Senior Scientist

Scion - Next Generation Biomaterials

49 Sala St. Rotorua

Private Bag 3020, Rotorua 3046

NEW ZEALAND

Ph: 64 7 343 5581

Fx: 64 7 343 5507

www.scionresearch.com

 

 

 

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of [hidden email]
Sent: Saturday, 23 January 2010 1:59 a.m.
To: [hidden email]
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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