Dear Luna,

If I understand correctly, you are trying to measure the area of a specific object in the image. You can do this in ImageJ by creating a selection and then using Analyze -> Measure. This will get you the area in pixels, which you can calculate over to metric units if you know the scale for your image (or you can set up the scale directly in Analyze -> Set Scale). You can specify what to measure in Analyze -> Set Measurements.

You don't need to convert to vector graphics for area measurements.

Here is a good summary on measurements and setting the scale: http://serc.carleton.edu/eyesinthesky2/week2/get_to_know_imagej.html

Hope this helps,

Eszter

Hi Luna,

Thanks for the question.

Are you trying to measure 2D areas from objects in the image, 2D perimeter lengths from objects in an image, or trying to estimate 3D surface of an image from a 2D image. If it is the latter, I am afraid that will not be possible without taking at least one other image from a different perspective, so that you could use parallax between the two different viewpoints to estimate depth, and thus, surface area.

Would you be able to post an example image you are working with. This will help us better answer and understand your question,

Cheers,

John

Dear Eszter and John,

Thank you both for your answers. 

I have attached one of my photos. I am trying to measure 2D surface area, but as the photo shows, the shapes of the macroalgae are quite complicated and not simple leafs. The problem with ImageJ is that I cannot manage to make a precise selection of the area I want to measure. When I sharpen the contrast and then select an area with the magic wand, it makes one big selection of the outer edges, including all the white areas inbetween the branches. Therefore I tried to convert it to a vector. That was more precise, but still not precise enough, as the tips of the branches often missed, and these algae grow in the tips.  

Is there perhaps a way to select a more precise area in ImageJ?

Cheers,

Luna

Hi Luna,

Thanks so much for posting the images. As is likely obvious from my many other posts, I prefer not to use ImageJ, as we have a developed MIPAR (http://MIPAR.us), a product which I and many other users believe is next-gen powerful, flexible, yet surprisingly straightforward image analysis software. Just about everyone who encounters a problem where they "tried to use ImageJ, but found it too difficult or impossible to do X", loves their experience with MIPAR, and as such, I have been implored by our users to aggressively spread the word.

I put together a Recipe file which automatically finds and measures the area of your algae sample. The speed of the Recipe will vastly improve if a cropped area closer to the algae were used (or if the image were resized even a little - you could easily add a crop or resize step to the top of the recipe, but I chose to leave it out to make the recipe more general). The precision will be even better some if their were no graph paper lines in the image. I know these are likely used for scale calibration, but if there were a way to include them in the image, without having them in the background of the algae, that would be best. I made the assumption that one grid square was 0.5mm in length, and this was used to calculate the calibration factor that is saved into the Recipe. Just open your image in the Image Processor, load the attached Recipe file, and you're done. You can then apply the same recipe (batch or one-by-one) consistently to other images. Recipes are very easy to tweak as well.

The Recipe relies mostly on the Adaptive Threshold step, which identifies algae pixels based on their being a certain level darker than what immediately surrounds then - a tool I think is much better suited to your problem than a basic global threshold, or the magic wand (i.e. region growing) tool. I am here any time for any questions, and would be happy to setup a 1-on-1 training any time as well at http://mipar.us/training. I have attached an image of the outlined algae finding, image of the overlaid algae finding, a screenshot of this result in MIPAR's Image Processor, and the Recipe file. Looking forward to hearing from you!

Cheers,

John

Impressive results with MIPAR, John!

Luna, in case you decide to go with ImageJ, I have attempted to replicate the processing steps John suggested (see attached results). You will need to download the Auto Local Threshold plugin (copy into ImageJ/plugins directory): http://imagej.net/Auto_Local_Threshold

0. Open your image in ImageJ

1. Image -> Color -> Split channels

2. Process -> Image Calculator...

        Red; Subtract; Green; Create new window

3. Image -> Adjust -> Threshold...

        Default; Dark background; Apply

4. Edit -> Invert

5. Process -> Image Calculator...

        Green; Max; Result of ...; Create new window

6. Image -> Adjust -> Auto Local Threshold

        Phansalkar; 15; 0; 0; Do not check "White objects..."

7. Process -> Binary -> Options...

        10; 6; Black background; Overwrite; Erode

8. Process -> Binary -> Options...

        10; 5; Black background; Overwrite; Dilate

You can then measure the area covered by the mask using Analyze -> Histogram, List (0 black, 255 white)

It is possible to automate the process for series of images using Macros, though it requires a bit of programming. For reference, see: https://imagej.nih.gov/ij/docs/macro_reference_guide.pdf

http://imagej.net/Introduction_into_Macro_Programming

http://imagej.net/Batch_Processing

https://imagej.nih.gov/ij/developer/index.html

Let me know if you get stuck,

Eszter

Dear Eszter and John,

Thank you very much for all your help and advice, both ways to calculate surface area seem to be very accurate. I have used Eszters solution with ImageJ and this works very well for my photos. Much appreciated! 

Cheers,

Luna

Eszter and John, the outcome is worth comparing for flexibility and versatility 

Hello John or Eszter,

I'm a bit new to image analysis software, but I'm trying to find something that I believe either program should be capable of doing. Essentially, I'm attempting to calculate the exact percentage of a given area within the whole surface area of a target object. Is that clear? For example, an image of a slide containing bacterial spores concentrated in a particular area. Is there a way I can highlight the area and then isolate each spore within that concentrated area in order to calculate what percentage of the concentrated area they inhabit?

Regards,

Kent

Hi Kent,

Thanks for the question. Absolutely MIPAR can make this very easy for you. If you'd like to attach an image to your question, we can quickly make a custom Recipe file which does what you need!

Cheers,

John

Hello Kent,

Depending on your image, you may be able to threshold it to mask/highlight the concentrated region, and then measure the total area of this region. To calculate the contribution of each spore to the total area of the concentrated region, you can then try the "Analyze Particles" command (ImageJ - Analyze menu).

For details, see: https://imagej.net/Particle_Analysis

For examples, see:

https://imagej.nih.gov/ij/docs/pdfs/examples.pdf

https://wangfanghelsinki.wordpress.com/2013/02/14/area-and-size-calculations-using-imagej/

Good luck,

Eszter

Hi Eszter,

Thank you for sharing your method to solve this problem (it was also my problem). I have another question: Can we crop (cut) an area of an image in ImageJ and change it scaled to a DWG file for plotter? In the other word, is ImageJ software able to work something like CAD systems? Currently we can do it by using SCAN2CAD or IMAGE2CAD software.

Hi Gholamreza,

ImageJ is primarily geared towards working with raster images (bitmaps) and not vector graphics. You can use thresholding, edge detection and tracing functionality in ImageJ to generate a binary image and a list of points representing contours in the image, and eventually save it as coordinates (in ROIs, regions of interests) or as for example .eps files, but I think this will be quite demanding to set up from zero and the results may come up short against other software.

If you are looking for free alternatives, consider the following list.

Potrace: http://potrace.sourceforge.net/

See also mkbitmap: http://potrace.sourceforge.net/mkbitmap.html

AutoTrace: http://autotrace.sourceforge.net/index.html

Delineate: http://delineate.sourceforge.net/

(provides a visual user interface for Potrace and AutoTrace)

Best regards,

Eszter

Hi Eszter,

Thank you so much for your help.

Best Wishes

Gholamreza

try using QGIS

Hi Eszter, Thank you so much for your help. Best Wishes

Use adobe photoshop.

Dear Eszter Agnes Papp ,

I have tried your method you posted above for calculating the area of the algae and seem to not get a solid white image that you achieved ( I have attached the final file for you to see). Do you know why this may be?

I have also attached the original image taken of my coral underwater. The tile is 14.8cm in length just for reference.

Any help would be greatly appreciated!

Thanks,

Kirsty

Dear Kirsty,

In case of your coral image, a different approach would work better (see attached images). You can use Image -> Adjust -> Color Threshold to get a decent selection for the coral (see settings on screenshot). There is a bit of extra area included at the base of the coral which can be easily corrected using e.g. the brush selection tool (second button from the left: "Oval, elliptical and brush selections", right click to switch to brush and then double click to set brush size). See attached RoiSet for results (open it onto your color JPG image).

After setting the image scale using the length of the tile as the known distance, the area occupied by the coral measures 38.706 cm2 (Analyze -> Set scale, Analyze -> Measure).

Hope this helps,

Eszter

Dear Eszter,

Thank you very much for you reply and for taking the time to help me.

So I previously played around with using the Color threshold option to select the coral; i'm just aware that with this method for measuring coral growth could be a bit subjective as the size will depend on how much I select each time I attempt to measure them? Ofcourse I could make sure I use the same settings but this wouldn't let me measure growth.

The method you suggested for the algae seemed to work well for my other individuals and worked better for the first coral I sent you when I cropped the original image and ran the method then (see images attached). I do like this method as it seems more objective to detect the edges of the coral for measuring every month.

I am a little unsure how you used the brush selection tool though to remove the base of the coral and then how you selected the whole coral outlined yellow as in your ROI file. When I tried it it, it just created a yellow shape around the base, but I dont know how you removed it? Sorry my skills in ImageJ still are not great! It would be good to know how to remove the base from the image so this isn't counted in the area/pixel number.

I really appreciate your help.

Kind regards,

Kirsty

ImageJ is only useful when the color is different.

You can also use a simple program call Sketch and Calc. It allows import of image and then you sketch in area with a tool and it calculates area and perimeter. The program has a trial period (online webpage) and costs US$10 per month or US$99 per year. Trial of the program is free

https://www.sketchandcalc.com