MANUAL

Important! - Image file recommendations:

You should use multi-channel image files like ZVI, CZI, LIF, AF or TIFF. Always use raw data format. Using jpgs or other compress formats will extremely distort your results.
The Focinator v2 names the output data and data means depending on the folder, in which your images are located (e.g. "C:\HEK293\treated\0.5 h 3Gy"). We recommend structuring your folders before producing the images. Doing this, you do not have to label each file and you can quickly generate large numbers of images!!

Installation and initialization of the Focinator v2
The Focinator v2 requires ImageJ version 1.51 bundled with Java 1.8.0 or higher. Copy the <focinator.txt> file into the “macro” subfolder of ImageJ installation folder. We recommend installing ImageJ to the folder C:\ImageJ. The new interface is based on a second script <Focinator-v2-23.R> written with programming language R. Therefore, installation of R-3.5.1 is necessary. Additionally, we recommend RStudio for comfortable handling of the R script.

Installation of Bio-Formats
To be able to open a broad spectrum of different file types we recommend the usage of the ImageJ Bio-Formats plugin. Download the <bioformats_package.jar> and copy this file in the plugins folder of ImageJ. The plugin parameters will be set automatically by the R script.

Please download the Focinator v2-23 files here.

You need ImageJ bundled with Java, Bio-Formats Importer and the R-3.5.1 language.

Focinator v2 installation:

Excel results sheets for further evaluation
After the automatic run, the result sheets will be in your chosen folder. You will find a collection of all means from all analyzed folders.

 

Please follow us on ResearchGate for latest news and patch notes!
researchgate.net/project/The-Focinator

 

Patch notes

:: v2.22/23
  • R-3.5-based problems were fixed.
  • New design of the report file
  • Channel names are now saved in the report file
  • Confirmation of the noise, cutoff, area, etc. values with “Enter” is no longer necessary
  • Fixed some minor stability problems
:: v2.10
  • All R-3.4-based problems were fixed. This includes both the installation of the graphic packages as well as those occurring during the runs and the data export
  • Fixed a problem that sometimes caused the ROI channel to be counted instead of the first foci channel on fast computers (detectable by intensity values of 255 in Foci channel 1)
  • Colocalization now works better and for all channels in both directions
  • It is now possible to type in your own channel names. These must be confirmed with “Enter”
  • Noise, cutoff, area, etc. values must be confirmed with “Enter” and are now transferred to the report file
  • The channel images and the progress window have been repositioned and are now always visible during the runs
  • Auto threshold method will now be saved for the next run and will be written in the Report file
  • The script has been simplified and cleaned up
:: v2.07
  • Increased stability
  • channel selection improved for large runs
:: v2.06
  • New function "Don't panic" for difficult images with high background/many cells -> extra 8-bit conversion of ROI channel
:: v2.05
  • Increased stability
  • all windows close command after last foci channel
:: v2.04
  • Increased stability
:: v2.03
  • Increased stability
  • correction of colocalization function
:: v2.02
  • Export of mean and max intensity values for all three foci channels
:: v2.01
  • New R-script-based GUI
  • 4-channel evaluation now possible
  • Colocalization now possible
:: v1.50
  • R-Script based automatic mode