Hi everyone.
I have thousands of images, showing the progression of a falling particle in slow motion, which I need to combine into a single image to create a visual track of the particle's progression. I have used an ImageJ macro to batch-convert the images to binary (the particle is black, the background is white). I have then converted the binary images to 32-bit TIFF and set v=0 to NaN. So for each image, the particle has a value of 255 and the background has a value of NaN. How would I then overlay all the images so that the particles are black and the background NaN values are white? Thank you so much for any help. |
Hi Jennifer,
if you don't have NaNs but a stack of binary images, you can use Image>Stacks>Z Project. If the particle has a pixel value of 0 (black) and the background is 255, the minimum of all stack slices will be black in all positions where you have a particle in any slice. If the particle has a pixel value of 255 (white) and the background is 0, the maximum of all stack slices will be white at positions where the particle has passed. With background value=0 and a nonzero value for the particle, you can also use the sum of all slices. The positions where the particle is in more than one stack slice will become brighter. http://rsb.info.nih.gov/ij/docs/guide/146-28.html#toc-Subsubsection-28.6.11 Michael ________________________________________________________________ On Feb 24, 2016, at 16:15, XBYJ wrote: > Hi everyone. > > I have thousands of images, showing the progression of a falling particle in > slow motion, which I need to combine into a single image to create a visual > track of the particle's progression. > > I have used an ImageJ macro to batch-convert the images to binary (the > particle is black, the background is white). I have then converted the > binary images to 32-bit TIFF and set v=0 to NaN. So for each image, the > particle has a value of 255 and the background has a value of NaN. > > How would I then overlay all the images so that the particles are black and > the background NaN values are white? > > Thank you so much for any help. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
That would work IFF all of the images will fit.
In case they don’t, I would consider: a) create a blank image - call it CumulativeImage b) use the Batch feature to add one image at a time to the CumulativeImage There are probably several ways to perform step b) - the simplest is probably to: c) create a stack containing the CumulativeImage and the next image in the sequence d) use Image>Stacks>Z Project e) save the result as “CumulativeImage” WE have found that Stack processing works really well for a small volume - but when the images get really big, or there are a lot of them, we have to revert to Batch to process the images one at a time. -- Kenneth Sloan [hidden email] Vision is the art of seeing what is invisible to others. > On Feb 24, 2016, at 10:41 , Michael Schmid <[hidden email]> wrote: > > Hi Jennifer, > > if you don't have NaNs but a stack of binary images, you can use Image>Stacks>Z Project. > If the particle has a pixel value of 0 (black) and the background is 255, the minimum of all stack slices will be black in all positions where you have a particle in any slice. > If the particle has a pixel value of 255 (white) and the background is 0, the maximum of all stack slices will be white at positions where the particle has passed. > With background value=0 and a nonzero value for the particle, you can also use the sum of all slices. The positions where the particle is in more than one stack slice will become brighter. > > http://rsb.info.nih.gov/ij/docs/guide/146-28.html#toc-Subsubsection-28.6.11 > > Michael > ________________________________________________________________ > On Feb 24, 2016, at 16:15, XBYJ wrote: > >> Hi everyone. >> >> I have thousands of images, showing the progression of a falling particle in >> slow motion, which I need to combine into a single image to create a visual >> track of the particle's progression. >> >> I have used an ImageJ macro to batch-convert the images to binary (the >> particle is black, the background is white). I have then converted the >> binary images to 32-bit TIFF and set v=0 to NaN. So for each image, the >> particle has a value of 255 and the background has a value of NaN. >> >> How would I then overlay all the images so that the particles are black and >> the background NaN values are white? >> >> Thank you so much for any help. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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