Image Particle Analysis - Color Code Particles

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Hello,

I use Igor to identify individual atomic columns in scanning transmission electron images of semiconductor crystals. The average intensity - obtained using the /D flag of ImageAnalyzeParticles - is linked to the composition of each identified column. I would like to place a marker on top of each identified column and have the marker color reflect the composition.

I use the M_rawMoments to place the marker at the center of each identified column and I have a wave that contains the compositions for all identified columns, but I cannot figure out how to map the marker color to the composition. Any suggestions?


My approach would depend on the total number of possible "compositions". If less than 10 I'd use a text marker instead. Otherwise, if you know the compositions why don't you try to use an annotation Tag or even a TextBox instead of a marker?

A.G.

January 18, 2016 at 01:05 pm - Permalink

A typical image contains in excess of 4000 atomic columns, so writing down the compositions is not the best option. I'd rather color code them and have a color scale on the side of the image. Furthermore, while it is relatively straightforward to interpolate the compositions and create a composition map, this map doesn't have any physical sense, as there is no matter between atomic columns.

I'll look into using a textbox and maybe changing the background color.

January 19, 2016 at 01:18 am - Permalink

kpantzas wrote:
A typical image contains in excess of 4000 atomic columns.

At this density you are indeed better off using colored markers. The problem is choosing 4k distinct colors and somehow mapping them into a meaningful scale of your composition data. To generate distinct colors you could simply try to start from 16-bit HSL wave where you keep the saturation and lightness at maximum and then evenly split the hue [0,65535] to 4000 levels. You then convert to RGB using ImageTransform.

A.G.
WaveMetrics, Inc.

January 20, 2016 at 11:06 am - Permalink

In the end I ended up creating an image that contained the computed value of the composition in a small rectangle area around the center of the atomic column and NaNs elsewhere. I then applied a colorcode to that image. Works fine, but the advantage of colorcoding Igor Graph markers is the autoscaling option... Anyway, thanks for the suggestions!

January 29, 2016 at 05:23 am - Permalink