Length measurement based on fluorescence intensity cutoff

Posted by wei.jian on May 25, 2018; 2:56am
URL: http://imagej.273.s1.nabble.com/Length-measurement-based-on-fluorescence-intensity-cutoff-tp5020732.html

Hi there,

I would like to enquire if there is any good quality check that I can
incorporate into my code for length measurement of a fluorescence image.

RefLineScan is a line scan of a linear structure with the indicated
intensity values. For length measurement, I would like to use 0.2 as the
cutoff. I.e. Pixel values >=0.2 will be considered as part of the length.
For the e.g. below, the length of the structure is 7 pixels.

Issue 1:
However, I realised that if the signal:noise of the image is poor, this
cutoff is not effective because hot pixels will be included as part of the
structure length. Hence, may I know if there's a good way whereby I only
consider a specific number of pixel as part of a structure length if
consecutive pixel values are above the set cutoff. I.e. Consecutive pixels
(for e.g. 3 pixels) need to have a value>=0.2 for them to be considered as
part of the structure.

Issue 2:
Apart from length measurement, I would also like to measure the relative
start position of the signal of interest. However, I'll encounter a problem
if the start value is observed more than once (for e.g. 0.21 is the start
value at position 2 but it also appears in position 8 of the array). May I
know if there's an easy way to ensure that I pick position 2?

//Start of code:
RefLineScan = newArray(0.11, 0.21, 0.31, 0.41, 0.51, 0.45, 0.35, 0.21,
0.15);
Array.show(RefLineScan);
                       
                        SingleCutOff = 0.2; //user defined cutoff
                        RefLineScanII = newArray(RefLineScan.length);
                        a = 0;
                        for (cut=0; cut<RefLineScan.length; cut++) {
                                if (RefLineScan[cut]>=SingleCutOff) {
                                        RefLineScanII[a] = RefLineScan[cut];
                                        a++;
                                }
                                startvalue = RefLineScanII[0];
                                if(startvalue == RefLineScan[cut]) {
                                CenStart = cut;
                                CenStartTab = Array.concat(CenStartTab, CenStart);
                        }
                }
Array.show(RefLineScanII);
Array.show(Array.trim(RefLineScanII, a));
CenWidth = a;
CenWidthTab = Array.concat(CenWidthTab, CenWidth);
Array.show(CenStartTab, CenWidthTab);
//End of code

Lastly, the reason why I used array.concat() is because this code is part of
a loop that measures length in multiple images. Array.concat() allows me to
have all the values in the same table.
Many thanks in advance.
WJ



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