Hi,
I am currently doing some analysis on a series of experiments I undertook. Each experiment involves approximately 3000 images. The experiments involve a liquid film flowing down an incline from a slot exit. I would like to measure the height of the liquid film in the region of interest so I can plot the values for the fluid flowing down an incline. So in effect I want take a number of slices every 0.001mm for around 15mm. An example image is attached with the light grey being the fluid that is coming from the slot exit and flowing down the incline. I would like to do this for each of the 3000 images as the film is unstable at the free surface and I would like to see how this changes over the time period the data was accumulated. At the moment they are single layer films, however in the future I would like to expand this analysis onto films of up to 3 layers.
I am currently using ImageJ/Fiji however so far I haven’t been able to work out an easy way to automate the process. Do you think it’s possible to do this kind of analysis in this program? If so do you have any recommendations for setting etc or techniques I can use to accurately measure my images.
Many thanks
If I understood you correctly you want something like this?
1) Apply a slight gaussian blur (this will flatten intensity fluctuations)
2) Perform a background subtraction
3) Make a straight line selection for your ROI
the image I added shows the plot profile along the line which looks almost like a perfect distribution kernel. Note: the background subtraction made the upper part of the image disappear, this is partially because it was saturated.
Now my idea:
1) Get the intensity values along the line and fill them into an array
2) normalize the intensities such that the peak is at 1 arbitrary units
3) Threshold out intensities lower than let’s say 0.1 arbitrary units
3) calculate the median and the 25%- and the 75%-quantile of the distribution
or alternatively the mean and the standard deviation
4) repeat this for the whole stack and output the results (q25, median, q75) into the results table
5) copy it to excel or save it as a CSV file
if this is what you need let me know, I would love to make that into a simple macro file for ImageJ.
Just out of curiosity:
Do you have all 3000 images in a single stack? A virtual stack might be a much better solution or having single images in a folder.
Is the ROI always in the same place of the image?
It might not be the answer you are looking for, but I use imagej to process stacks of pictures. It is a useful tool, and you should be able to do what you want in it.
Best regards,
c s a b a
Dear Richard,
If I understood well, you wanna automate an image processing algorithm with ImageJ. To do so, you've got to create a Macro. This is actually quite simple. The best way to start with this tool is the Record plugin (Plugins > Macros > Record). This tool opens a window in which every action you make is recorded. After making all required operations, you can create the macro with the Create button. Then, you just have to save the macro with a .ijm extension. To launch the macro, open it with ImageJ and press Ctrl+R.
For a stack of images, you can use a FOR loop that opens every image of the stack one by one (see the document : http://rsbweb.nih.gov/ij/docs/macro_reference_guide.pdf).
As for the single image you provided us, I wrote a simple macro to generate a binary image highlighting the different layers. It also creates a .txt file in which values (0 or 255) are ranged according to X and Y coordinates (available from Analyze > Tools > Save XY Coordinates). This can be useful for processing images in Matlab for instance. In the macro, you have to write down the folder locations where your image is, as well as the locations where you want new files to be saved. I added comments in the Macro.ijm file.
From this binary image (Mask of Image.jpg attached), you must be able to measure the different heights at different locations, for example with the tools presented by Martin Jakob.
Please feel free to ask more questions if any point isn't clear enough.
Good luck,
Paul
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