Version 1.2.x     Bureau H. Glünder 2019 / 2020

WHAT FOR

Easy Focus is an “ImageJ”-Macro that returns the best focused slice of a stack that represents a focus series. The stack may contain a single focus series (z-stack), a temporal sequence of focus series, or focus series of colour channels (4D-hyperstacks).

Easy Focus requires stacks of square-sized image-support or selection (ROI).

Easy Focus-analyses are RGB-agnostic and cannot be applied to 5D-hyperstacks.

 

INSTALL

Download “EasyFocus_1-2-x.zip” and unzip it.    ( Step-by-step installation guide for “Fiji” )

Launch “ImageJ” and install the file Focus_LP.class per menu item “Plugins ▹ Install...” or move it to the “plugins”-folder of your “ImageJ”-installation.

Move the file Easy Focus.ijm to the folder “ImageJ ▹ plugins ▹ macros”.

• Do not copy the file to the folder “ImageJ ▹ macros”!
  If the folder “macros” does not exist in the folder “plugins”, then create it.

Quit and re-launch “ImageJ”.

 

HOW TO

Open an image-stack holding a single focus series, or a 4D-hyperstack holding a temporal sequence of focus series, or a 4D-hyperstack holding focus series of colour channels. The stack images or a selection (ROI) thereof need to be square-sized. (Please note that if your stacks do not conform to this size restriction, you may create conforming selections or regional analyses.)

ImageJ : Choose the item “Easy Focus” from the “Plugins”-submenu “macros”.

Fiji :        Choose the item “Easy Focus” from the “Plugins”-submenu “Macros”.

Result:

• The returned 16bit image or image-stack shows the slice(s) that is/are determined as being best focused with respect to the analysis of the whole image or of the indicated selection (ROI).
• Its/their position(s) in the original stack is/are displayed in the subtitle bar(s).
• Important note:
  The best focused slice needs not be perfectly in focus because it merely is the relatively best focused slice of a focus series according to a kind of spatial majority decision regarding the focus of the slice or selection. Consequently, the results will strongly depend on the depth-resolution of the focus series and on the image content.
  Especially for imaged 3D-objects, regional focus analyses (using small ROIs) provide more meaningful results than global ones.

Details:

• Please consult the description of the “ImageJ”-Plugin Focus LP that represents the core of “Easy Focus”.
    (“Easy Focus” uses the “Standard”-criterion with “Size 9”-kernel.)
• For different parameter settings, hold down the “alt”-key when launching “Easy Focus”.
    (Changed parameter settings are not persistent.)

 

TERMS OF USE

Easy Focus may be used without a license.

 

Easy Focus is NOT in the public domain.

 

Easy Focus may NOT be sold.

 

Easy Focus is provided AS IS and you use it entirely at your own risk.

 

Easy Focus calls an “ImageJ”-Plugin that comes with “EasyFocus_1-2-x.zip”.
  Its “Terms of Use” etc. can be accessed from ReadMe_FL.

LEGAL INFORMATION

• “Easy Focus” is copyright-protected 2019/2020 by Bureau H. Glünder.
• “Easy Focus” may be used without acquiring a license and it is definitely not allowed to sell it.
• “Easy Focus” may not be (re-)distributed without the above “Terms of Use” and this “Legal Information”.
• If the source code in file “Easy Focus.ijm” is altered and distributed, the above “Terms of Use” must be maintained and included with the altered code.  It must also be mentioned that the altered code is based on copyrighted code of Bureau H. Glünder and that changes have been made.
• “Easy Focus” is given away AS IS.  It is solely the responsibility of the user to determine the software’s suitability for a particular purpose or use.
• Although “Easy Focus” has been developed with great care, you use it at your own risk.
• Bureau H. Glünder cannot be hold responsible for any kind of direct or indirect damage or loss—including but not limited to, any interruption of service, loss of business, loss of profits or good will, legal action, or any other consequential damages—that may be caused by installing, configuring or using “Easy Focus”.
• Because the source code in file “Easy Focus.ijm” can be arbitrarily modified at any time and to any extent, Bureau H. Glünder has no control over its state and its use.
• “Easy Focus” is not a stand-alone software. It fully depends on “ImageJ”-software modules and their state of installation and development.
• By using “Easy Focus” the user agrees to the generally accepted fact that to date flawless software cannot be guaranteed.  Hence, imperfect software is not faulty in the legal sense.  “Easy Focus” may contain “bugs” that limit its use or even make its use impossible.