Hi, is there a way for me to change the values that are being reflected in my calibration curve? Most of my values are on the lower end of the scale bar and I would like to focus on that region. Thanks!
Your image seems to hold only one colour, despite it being colour, you can call this monochrome.
Sample your scale bar at known locations and with fill out the known values. Then choose an appropriate values as shown in the calibration strip, then do a calibration using an appropriate function. I chose linear and came up with the following macro. Interpolation can be done if the calibration is valid. If the linear function is the proper one, I’m not sure… a 2nd degree polinomial has a better R2 value.
If you want a calibration focused on the lower values, you need to make a ‘longer’ calibration strip, with more known values in that region. That improves the validity of that part of the scale. In the numeric part of your scale, it is not clearly indicated where these pH’es are exactly. I just chose a few that ‘seemed’ good.
Does this answer your question?
run("8-bit"); //setTool("point"); makePoint(1045, 257, "small yellow cross");run("Measure"); makePoint(1046, 213, "small yellow cross");run("Measure"); makePoint(1046, 169, "small yellow cross");run("Measure"); makePoint(1046, 130, "small yellow cross");run("Measure"); makePoint(1045, 89, "small yellow cross");run("Measure"); makePoint(1046, 48, "small yellow cross");run("Measure"); run("Calibrate...", "function=[Straight Line] unit=[Gray Value] text1=[221.00 191.00 165.00 104.00 48.00 4.00 ] text2=[6.7 7.98 9.26 10.54 11.82 13.10] show");
thank you for your reply! may i know where the values at text1 in your macro are taken? are these the pixel measurements? sorry, am new to imagej so it’s taking me awhile to figure things out… thanks!
The macro records intensities at points as per MakePoint(x,y), from the image I copied from this forum message and put into ImageJ New>System Clipboard. Better would be to have taken a rectangular ROI of the strip’s width and height 1, but this was faster.
If you then choose to Calibrate, the Measure’d values are already in the left column of the table, I filled out the ‘known’ values that I read from the numbers next to your calibration strip at locations I thougt to be valid, into the right column and hit OK. All of this was performed while Plugins>Macros>Record… was active, which I then copied and pasted into my forum answer.
So the text1 was generated by the makePoint which was generated by me pressing the mouse while the Point tool was active.
got it, thanks for the help!!