This tool will propose several processes for the automatic segmentation of images. Have a look at the project's Cancer Feature Analysis to get more information about the image analysis tools.
In Fiji window, open Plugins > Macros > Startup Macros... and copy and past the code >> here <<. Change the language into IJ1 Macro and save as .ijm file in the Fiji.app folder > macros > toolsets.
Select the tool in the "More Tools" menu (>>)
- HELP
Summary descriptions of the tool's tabs - Image Segmentation
Apply the choosen segmentation algorithm to delineate contourn (right click for open a dialog box to choose one algorythm and change parameters). - Core Area
Apply the segmentation algorythm to delineate core contourn (right click for open a dialog box to choose one algorithm and change parameters). - Skeletonize
Skeletonize from a binary ROI (Requires having the ROI of the total area in the last position in the ROI manager).
A. Step-by-step presentation of the segmentation: (i) Raw image ; (ii) Image obtained from the subtraction of the filtered image by the image with a mask ; (iii) Contour of the image with Sobel filter ; (iv) Delineation of the different zones of the spheroid. B. Examples of segmentation with basic parameters. Scale = 50 μm.
Source: Joris Guyon. Nouveaux mécanismes du développement des tumeurs cérébrales. Biologie cellulaire. Université de Bordeaux, 2021. Français. NNT : 2021BORD0344 . tel-03576571
To try this macro, you can find samples here.
Guyon, J., Fernandez-Moncada, I., Larrieu, C., Bouchez, C., Pagano Zottola, A., Galvis, J., Chouleur, T., Burban, A., Joseph, K., Ravi, V., Espedal, H., Røsland, G. V., Daher, B., Barre, A., Dartigues, B., Karkar, S., Rudewicz, J., Romero-Garmendia, I., Klink, B., Grützmann, K., Derieppe, M-A., Molinié, T., Obad, N., Leon, C., Seano, G., Miletic, H., Heiland, D., Mariscano, G., Nikolski, M., Bjerkvig, R., Bikfalvi, A., and Daubon, T.
Lactate dehydrogenases promote glioblastoma growth and invasion via a metabolic symbiosis. EMBO Mol Med (2022) e15343, doi.org/10.15252/emmm.202115343.
This toolset was developed on window 10, and tested using ImageJ v1.53. Many features require installation of command line tools that may present future challenges on different operating systems.