How to create a cartography

[Louise]

Hi everybody,

i am a casual user of imageJ for very simple tasks but recently I have a new project and I don’t know if ImageJ can be used in this situation.

I have a material that was compressed :

!
I would like to know approximatively the size and the orientation of the beads. So I threshold and binarize my picture and use the ellipse split plugglin (which is very useful) and then I obtain the long and short axe of each ellipse, their aspect ratio, and their orientation.

But then I would like to colorize the ellipse on the picture depending on the aspect ratio so I would be able to see if there are some preferential directions of compression. (diagonal bands on the picture where the aspect ratio is larger)

Do you think this work of cartography would be possible with ImageJ (or Fiji of course) ? I tried to first find how to put the values I obtained in order (depending on the aspect ratio) but I couldn’t find how to do it.

Thank you very much for any guidance you can offer a novice like myself!

[anon96376101]

Good day Louise,

I don’t know this plugin that does the fitting of ellipses but if the ellipses are selections (ROIs) or overlays that can be listed in the ROI manager, then you could color them to your liking. You need to invent a nice coloring scheme.

Here is a thread that deals with a closely related topic;
http://forum.image.sc/t/undo-on-overlay/7719/6?u=herbie

Regards

Herbie

[Louise]

Hi Herbie,

The ellipses are indeed selections. Thank you very much for the example, I searched in other topics before asking for help but I couldn’t translate my problem in suitable keywords.

(For others who could be interested, I’ll publish my solution as soon as I find it. )

Thanks again for the help and the reactivity !
Regards,

Louise

[dlegland]

Hi,

just wanted to mention the “Assign Measure To Label” plugin in the MorphoLibJ suite. It requires a data table and a label image (the latter can be obtained for example by connected component labeling on binary image). The plugins allows to choose the column containing the result to visualize, the label image, the color map, and the value bounds for adjusting colors.

Small example on elongation computed on a binarisation of the blob image, and fire LUT:

Maybe not the only way to do it, but I wanted a quick way for generating such results…

David

[Louise]

Hi,

This plugin is indeed a very good solution for my problem.
I added it to my Fiji menu and tried to use it after the ellipse split plugin but I have some problem obtaining a colored map, so I still need to figure out how everything work.

This is before the MorpholibJ plugin but after the ellipse split plugin

My Label Map has the good settings

But when I click on “ok”, my first picture become orange

Anyway I tried then to use the “Assign Measure To Label” plugin as you suggested, but all I obtained is a picture with a black background and grey cells with no variations.

And when I directly use “Assign Measure to Label”, and change afterward the label map, I obtain all the cells in the same color

I know I am not doing something right (maybe the label images ?) but I still need to work on it.
But I think once it is done, it will be exactly what I need !

Thank you for your help !

Louise

[dlegland]

The Colorize Label plugin requires a Label image as input, i.e. an image whose each pixel value correspond to the particle number (or 0 if it is background). You an obtain it buy applying “Connected Components Labeling” on the binary image.

Some caveat: you need to ensure that labels obtained from CC labeling and row indices in table are consistent. It should be the case if the binary image is not too much noisy (particles touching by corners may be recognize a one label with one algorithm and several label with other algorithm…)

[Louise]

Assign Measure To Label” plugin

Dear dlegland,

Sorry I did not gave you an answer right away. The CC labeling worked but I had some problems matching the CC labeling and row indices. But I think with Erode cycles then some dilate ones, I am able to obtain something to work on. (here the color depends on the angle of the particle)

Do you think it is possible to add a color scale on the picture ? Otherwise I will do it manually, because it makes the picture clearer.

Thank you for you kind help,

Louise

[dlegland]

Hi,
Do you mean adding a colorbar as surimpression on original image, like a scale bar? Hmm… should be possible, but not sure I will have time to do it soon… I’ll think about it anyway!
David

[Louise]

Hi,

Yes, a scale bar, that’s it. But it was just an idea, no need to worry about it.

Louise