Getting the blues from NAM01 - an example

Last update 22 March 2020.

This is NAM01 - a sample from a Scots pine growing on the island of Nämdö. Soxhlet treating, sanding and polishing and scanning was managed by Ryszard J. Kaczka and Karolina Janecka. The soxhlet treatment is evident from the light surface. The brown tar has apparently been removed through the soxhlet process.

The .pos file is available here NAM01HZ.pos and the .jpg file here NAM01HZ.jpg

The measurements in the .pos file have been done in CooRecorder with a reference curve as a necessary support as there is a big number of false or almost missing rings. A suitable reference is NamdoAll.wid. You can also create your own reference from the ITRDB swed302.rwl collection.

ToDo: In your browser, copy the link location above for "NamdoAll.wid".
In CooRecorder, click the menu command "File/Enable ring width curve display".
If there is then an "Open file dialogue", paste (Ctrl-V) that link into the File name field.
If no dialogue opens, click the menu command "File/Select Reference .wid or .pos file" and then paste the link into the File name field.

Now open the .pos file: In your browser, first copy the link above of NAM01HZ.pos. Then click "File/Open coordinate file (.pos file)" and paste the link into the File name field and click OK.

The NAM01 red and green curves will now overlay the reference curves. If they are not in synchronized position, click the "Click for CorrC!" button above the curve diagrams. Click the "Fit on screen" icon at the top of the screen to make the image somewhat larger. You should now see something as shown above.

We are now set up for collecting some blue data!

Click the menu command "CI-measurements/Settings for color intensity (CI) measurements and calibration"
We will set up two CI collectors. The first one is shown above. See that you have the same settings in CooRecorder. This first CI collector is set up to collect and save latewood inverted data which should crossdate towards ring widths.

This is for the second CI collector which is set up to collect earlywood blue data for use to create a "delta-blue-file" as a difference between this earlywood data and the latewood data collected by CI collector number 1.
Please see that both CI collectors number 3 and 4 are disabled! (Their numbers are then NOT underlined as shown above)
Out of this we expect to get TWO .wid files, one with inverted blue latewood data and one with delta-blue data. When ready click OK to close this settings window.

To avoid having the curves diagram in our way, we close that window by unchecking the menu command "File/Enable ring width curve display (Ctrl-Tab)"
Also select the Zoom-in icon (Z) and click in the image until the magnification is about 70% - Now we are prepared to create the blues!

Click the blue "lb" icon!

The window which popped up (above) is used in two alternative ways:

  • For testing EACH enabled CI collector separately, normally without saving the data.
  • For automatically running each enabled CI collector one after the other and then saving the data in .wid files.

With the settings above, we click OK to start testing CI-collector number 1.

Blue areas are considered to be latewood. The dark blue areas are those selected for retrieving blue data. You have to scroll through the whole image and see that all blue areas are layed out correctly. When they are overlaying with a neighbour area you might have to (if possible) adjust the position of the ring border point (the numbered point).

In case you want to save this latewood blue data, you have to click the menu command "File/Save CI measurement .wid files AND .pos file if unsaved"

To check also where the earlywood CI data is collected we once again click the blue lb icon and select CI collector number 2 as shown above and then click OK.
The blue areas in the picture above indicate where earlywood data is collected. Also in this case you have to look through the whole sample and see that there are no or few overlapping color spots.
Finally we again click the blue lb-icon and then check "Run ALL enabled CI collectors..." In this case the blue colored spots cannot be plotted as they would otherwise overwrite each other as we are running two CI collectors, one after the other. Click OK to start the calculations.
Click OK to save your two .wid files!
The two .wid-files are presented.

Opening the files in CDendro

In CDendro, see that you open your three .wid files and also the .pos file. Select NamdoAll.wid as your reference. (NamdoAll is a mean value of many detrended ring width samples)
    We will
  • first compare the .pos-file (Nam01Hz.pos) with the reference.
  • Then compare the delta blue with the reference
  • Then the inverted-latewood blue file with the reference and finally
  • the delta blue file with the ring-width .pos file
"RingsToRef": CorrCoeff = 0.68 between normalized curves. 0.52 between REF and non-detrended ring width curve.
"DeltaBlueToRef": CorrCoeff = 0.70 between normalized curves. 0.60 between REF and non-detrended blue delta curve.
"LatewoodBlueToRef": CorrCoeff = 0.55 between normalized curves. 0.52 between REF and non-detrended blue latewood curve.
...and finally DeltaBlue compared to the .pos file (the ring widths). They look very much the same! Does the blue really tell something more than the ring widths?

What's next?

The intention with this lecture was to demonstrate how you can retrieve blue channel data with the help of CooRecorder. Hopefully you can now start to adjust parameters and thus experiment with other settings than those used above.

If you are new to using CooRecorder, I recommend you to study all "help lectures" available at this site.
Though at first you may very well disregard the sections on colour calibration. To be able to export your data to other dendro programs for your analysis, you should also make yourself acquainted with CDendro where you will find powerful mechanisms for crossdating and organization of your data.

March 22 2020
Lars-Åke Larsson, Cybis Elektronik & Data AB, Sweden. www.cybis.se



Copyright © 2020, Cybis Elektronik & Data AB, www.cybis.se