Extended depth of focus is useful for imaging deep objects where you want to see the whole thing in focus.
The lens on this microscope has a very shallow depth of field, therefore, if you focus at any plane in a cm deep object, the rest of the object will be out fo focus.
Extended focus is when you collect a Z series and set the software to combine the images only with the in focus elements.
For instance, in this example two pairs of scissors are lying on top of each other and we are imaging the tips. We collected 45 images at 190 micron steps in Z. You can see that when blades at the bottom are in focus, the blades at the top are out of focus and vice versa.
The extended focus image retains only the in focus features. Note that there is a scalebar on the image. This is important any time you show an image. CZI files have the scalebar information retained inthe metadata and ImageJ automatically reads and assigns this.
Extended Depth of Focus maybe set to operate directly as the images are collected or may be applied afterwards.
We have found that Variance and shift correction are the best methods.
