Artemia Tools

The Artemia Tools help to calculate the normalized redness of Artemia in images like these: artemia1, artemia2 and artemia3.

License: CeCILL-C

Getting started

To install the tools, drag the link MRI Artemia Tools.txt to the ImageJ launcher window, save it under macros/toolsets in the ImageJ installation and restart ImageJ.

Select the "MRI Artemia Tools" toolset from the >> button of the ImageJ launcher.

  • the first button openes this help page
  • the p-button prepares the image by creating an rgb-stack
  • the m-button measures one specimen in the image
  • the n-button opens the next image in the folder
  • the c-button asks for the red-reference region and calculates the corrected redness of the specimen measured before


  1. Use File>Open to open the first image you want to analyze in the folder with your input images.
  2. Press the p-button. This transforms the opened image into an RGB-stack and opens the threshold adjuster.
  3. Select the first specimen - you can do this by adjusting the upper-threshold value in the threshold tool (best seems to be to select Over/Under display mode) and then when everything around the specimen is green, click on the specimen with the magic wand tool from the ImageJ launcher window.
  4. Add the specimen-selection to the roi-manager by pressing 't' (the roi-manager will be opened if necessary).
  5. Select the part to be subtracted from the selection. First use control+shift+a to delete all rois from the image, then adjust the lower threshold and use the magic wand tool or make a manual selection using the freehand-selection or another selection tool. Zoom into the image to make a good selection. The selection can consist of multiple parts, in this case hold down shift when adding parts to the selection. Hold down alt to delete parts of a selection.
  6. Add the selection to be subtratced to the roi-manager by pressing 't'.
  7. Press the m-button on the toolset to measure the intensities in the three channels. This will open the results table and add the measurements to it.
  8. Go to the next specimen in the image (you can drag the image by holding down space-bar, clicking into the image and moving the mouse.). Repeat the procedure from step 3.
  9. When all specimen of an image are measured, press the c-button to calculate the redness-values. Click the c-button. Select a region in the red-reference area and press the ok button of the "Action required" dialog. This will write the raw-redness the normalized redness and the mean-redness-value of the normalization area for the current image into a new results-table.
  10. Press the n-button to go to the next image and repeat the procedure starting at step 2
  11. When all images are measured transfer the results into a spreadsheet-application either by using copy and paste or by saving a file and using the file-import in the spreadsheet application.

Publications using the tool

  1. Rode NO, Lievens EJP, Flaven E, Segard A, Jabbour-Zahab R, Sanchez MI, et al.
    Why join groups? Lessons from parasite-manipulated Artemia.
    Ostfeld R, editor. Ecology Letters. 2013 Apr;16(4):493–501.

Test07042011106.tif - example image 1 (35.1 MB) Volker Baecker, 07/04/2013 02:05 PM

Test07042011107.tif (35.1 MB) Volker Baecker, 07/04/2013 02:08 PM

Test07042011108.tif (35.1 MB) Volker Baecker, 07/04/2013 02:11 PM

mri-artemia-toolset.png (1.22 KB) Volker Baecker, 07/04/2013 02:35 PM

artemia-input.png (242 KB) Volker Baecker, 07/04/2013 02:57 PM

results.png (3.4 KB) Volker Baecker, 07/04/2013 02:58 PM - the artemia test images (26.8 MB) Volker Baecker, 09/13/2017 04:02 PM