Below are some handy tips for working with CoLocalizer Express:

Try Auto mode first. Choose preset depending on the pattern of your image. If your image has low contrast or weak fluorescence, click Low Contrast or Weak Fluorescence radio buttons respectively. If the image is average contrast and fluorescence, use the default Average Contrast and Fluorescence preset. There is no need to reset image if you want to try another preset.

If the results of your calculations look highly suspicious and/or they do not correspond to the values of Pearson's correlation and Manders' overlap (R) coefficients (less than -1.0 and/or more than 1.0 for Pearson's coefficient and out of the range from 0 to 1.0 for Manders' coefficient), switch to Manual mode. In this mode, the most efficient way to correct background is to use Threshold Value for all channels. Select All Channels, choose the number, and click Apply. If you see that background was corrected incompletely, choose bigger number and click Apply again. If after you did it you see that background for one of three channels is still corrected insufficiently, select that channel and adjust background correction for the selected channel.

Remember to use background correction settings consistently when analyzing images in the same study.

Although Pearson's correlation coefficient (Rr) is a CoLocalizer Express default coefficient, Manders' overlap coefficient (R), indicating a true degree of colocalization, is very useful too. In fact, it may be even more suitable if your sections are not freshly stained and/or your images were obtained after re-examining samples.

To open image quickly, drag and drop it onto CoLocalizer Express icon - just hold down Command-Option keys while you drag. You can drop image onto any CoLocalizer Express icon, whether it is in the Dock, in the Finder's sidebar, or in the Finder itself.