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
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