12.2 C
New York
Monday, March 27, 2023

2 Crucial Strategies to Show Overlap

Microscopy, by default, is a method that permits us to look at, moderately than measure, organic occasions and make conclusions primarily based on what we see moderately than on some calculations.

Generally, although, our observations should meet sure standards to assist our conclusions.

This text offers with measuring the situation essential to so many protein analysis areas: protein colocalization.

Learn on to find two methods you may quantify and show it.

Why Is a Visible Willpower of Colocalization Inadequate?

Whereas there are conditions the place you may decide protein colocalization visually, a extra correct affirmation of a mutual distribution of two probes is normally mandatory to attract incontrovertible conclusions.

Solely whenever you acquire pictures following a managed protocol for colocalization evaluation (with ample sign in every channel, no autofluorescence or sign bleed-through) is it protected to say that the 2 probes colocalize solely primarily based on statement.

In such instances, if the inexperienced sign colocalizes with the crimson sign and the image is generally yellow, no statistical measurement is required.

However, when you don’t see an overlap, it doesn’t imply it isn’t there! For a visible instance of this, take a look at Determine 1 beneath.

An illustration of when visual inspection of protein colocalization is appropriate.
Determine 1. An illustration of visible inspection of protein colocalization (Picture credit score: Thomas Warwick.)

It may be that the intensities of the 2 channels are usually not the identical. That’s to say, the intermediate shade that we see can solely seem if each probes have the identical depth.

That’s why conclusions primarily based on visible willpower usually result in false unfavorable outcomes.

What Strategies for Overlap Measurement Exist?

Whereas there is no such thing as a one commonplace method to this matter, there are two strategies which are broadly used and usually accepted:

  1. Pearson’s correlation coefficient (PCC).
  2. Mander’s colocalization coefficient (MCC).

These two strategies relate to 2 totally different elements of colocalization—correlation and co-occurrence. [1]

Pearson’s coefficient is expounded to the correlation of the pixel intensities within the two channels. It measures the connection between alerts. Particularly, if the sign values in a single channel rise concurrently with the opposite, or one sign falls when the opposite rises.

Correlation is distinct from co-occurrence, which is mathematically expressed by way of Mander’s coefficient. [2] This represents the protection of 1 sign over the opposite, which reveals the extent to which two probes occupy the identical place. Let’s discover this a bit additional.

Two Strategies to Show Protein Colocalization

1. Pearson’s Correlation Coefficient (PCC)


PCC displays the linear relationship between sign intensities.

The values can vary between 1 (excellent constructive correlation) and -1 (excellent unfavorable correlation).

A price of 0 signifies that there is no such thing as a correlation. It’s doable to discover PCC visually by way of a scattergram the place the coordinates on the plot characterize pixel values (sign) in each channels. The extra dots that cluster round a straight line, the higher the correlation between the 2 alerts

Necessities and Issues

The PCC needs to be measured within the area of curiosity (ROI) to keep away from false positives or negatives. If measuring PCC over your complete picture, pixels of the background will correlate completely and inflate the PCC.

In distinction, if the measurement is carried out in a area of no curiosity with a heterogeneous distribution of each channels, the PCC can be depressed.

You possibly can choose ROI by hand or by thresholding to exclude the background.

Whichever manner you do it, watch out, particularly when thresholding.

The collection of the ROI wants to incorporate all of the related areas of the cell(s). That’s each place the place a probe may be anticipated to distribute.

In case you use an intensity-based technique for choosing ROI (thresholding), you would possibly inadvertently exclude related outcomes.

How can this occur?

You might have a area of mutual exclusion the place neither label seems. This is usually a biologically related outcome (each molecules are usually not expressed in that place within the cell). Nonetheless, thresholding won’t embrace this area within the ROI, placing you in peril of dropping related outcomes.

When is Pearson’s Correlation Coefficient Really helpful?

PCC needs to be used on pictures the place you count on a linear relationship between intensities.

If the information matches a extra advanced mannequin, PCC won’t carry out properly.

A unique technique also needs to be chosen if there’s an uneven overlap, the place probes co-distribute however in numerous proportions. This will likely happen when GFP is used as one probe. Its expression stage could differ between cells and probably trigger despair of PCC resulting from excessive intercell variability.

2. Mander’s Colocalization Coefficient


MCC is a metric that describes co-occurrence—the fraction of 1 protein that colocalizes with the opposite.

MCC provides you with a very good measure of colocalization whenever you label one protein in a vesicle and need to see the way it colocalizes with a selected construction in a cell, say a microtubule.

If we assume that every one vesicles colocalize with microtubules, however solely a proportion of microtubules colocalize with the vesicle, you may calculate MCC for every channel and get a metric that quantitatively describes this fractional overlap.

Necessities and Issues

The catch with MCC is that it requires the elimination of background.

The trickiest half right here is setting a cutoff level for the depth that allows background subtraction.

MCC measures the entire fluorescence of 1 probe in each above-zero pixel. Nonetheless, above zero pixels are extraordinarily uncommon due to elements resembling:

  • Autofluorescence.
  • Gentle leakage.
  • Non-specific labeling.
  • Fluorescence from out-of-focus picture plains.

The measurement of MCC, subsequently, requires a cautious collection of the brink (cutoff).

A technique to do that is world thresholding, the place you subtract a threshold worth from every pixel so that each stage beneath the chosen cutoff can be background whereas each pixel above will fall right into a area of curiosity.

Whereas that is intuitive, world thresholding is crude and should result in undesirable conditions like excluding low-value pixels which are near the background however are in actual fact constructive and actual information.

A extra computerized and fewer subjective possibility is the so-called Costes technique, the place the brink is estimated by calculating PCC a number of instances.

This serves to outline the vary of pixel values which are constructive and, subsequently, shouldn’t be excluded. PCC is calculated for various teams of pixels, and the pixel values for which PCC is the same as or near zero are taken as the brink values.

However, it also needs to be checked visually since in pictures with a decrease signal-to-noise ratio, it might establish a threshold stage so low it doesn’t distinguish labeled buildings from the background.

When is Mander’s Colocalization Coefficient Really helpful?

When the organic query of your experiment issues the extent that proteins and mobile buildings overlap, MCC needs to be the measure of selection.

These coefficients are extra intuitively interpreted than PCC and are impartial of sign proportionality (the variations within the variety of buildings labeled by every probe).

Be Goal and Management as Many Parameters as Attainable

Whichever selection for measuring colocalization you go for, it is rather essential that the picture assortment is carried out within the appropriate manner. And ensure your statistical evaluation of your protein colocalization information is legitimate. [3]

Attempt to management as many elements as you may, and put together a set of management samples that will let you monitor as many variables as doable.

Understand that visible colocalization willpower is influenced by many elements, together with:

  • Observer subjectivity.
  • Every particular person’s mind processing colours in a different way.
  • Attainable shade blindness of the observer.
  • The spatial decision figuring out the pixel dimension.

Amongst many others. So make sure to course of the photographs you’re about to investigate uniformly, and keep in mind that any uncontrolled manipulation could trigger you to lose related data.

Preserve Your Software program As much as Date

These calculations are applied in most picture evaluation software program packages, resembling ImageJ and Volocity. However, on condition that measuring colocalization remains to be a considerably confounding area, enhancements are required, so maintain monitor of the brand new variations and packages for the software program.

Protein Colocalization Summarized

So there are two strategies to quantify and show protein colocalization.

The PCC technique lets you analyze colocalization information when it matches a linear mannequin. And the MCC technique lets you analyze fractional co-occurrence information for extra advanced datasets.

Plus, we’ve coated elements to concentrate on that cut back the objectivity of your observations.

Helpful eh!

Is there something particularly that you just do when measuring protein colocalization? Tell us by writing within the feedback part beneath!

Initially printed Could 2018. Revised and up to date January 2023.


  1. Dunn KW, Kamocka MM, and McDonald JH (2011) A sensible information to evaluating colocalization in organic microscopy. Am J Physiol 300(4):C723–42
  2. Adler J and Parmryd I (2012) Colocalization Evaluation in fluorescence microscopy. In: Cell Imaging Strategies: Strategies and Protocols, 2nd version. Humana Tototwa: New Jersey
  3. Mcdonald JH and Dunn KW (2013) Statistical checks for measures of colocalization in organic microscopy. Journal of microscopy 252(3):295–302

Share this to your community:

Related Articles


Please enter your comment!
Please enter your name here

Latest Articles