No sound on eg movie and question about edges

Hi

downloaded the demonstration of cellprofiler features but no sound even when run in VLC. the other movie works fine. is this just me?

also i have these images of rounded cells in brightfield on a mylar substrate. i’ve set the find edges which does find them but how do you exclude the ones that are to small? in image j you can set a scale on your images and set it to exclude everything below that. I’ve run the example of a human nucleus on these images but no joy really

i’m sure this is very simple but i am dim sorry. Plus I don’t really get your explanation of the pixels. when you open up an image how do you know how many pixels big your cells are so that you can exclude them. there is some measuring tool but i don’t get it.

cheers

charlie

Hi,

To see the size of an object, either go to ImageTools > Show pixel data and click and drag the pointer to see the length displayed, or click on the image and select Measure Length from the menu that pops up.

Since your images are brightfield, it’s no surprise that the example pipelines did not work well, since they demonstrate CellProfiler’s use on fluorescent images. However, you were correct to try FindEdges! I made a quick pipeline that does a pretty decent job using Illumination correction + FindEdges + IdPrimAuto, but still finds one spurious object. The problem is in the bright field images, dark spots look like cells, so getting a good illumination correction is important. You may want to try playing around with the microscope to get better illumination, if possible. This will make automatically identifying the cells with software much easier.

hope this helps!

~kate

And re: the audio, it initially sounded fine to me via Quicktime on my Firefox browser, however, indeed VLC seemed to have no audio. But this can be solved by going to “Audio -> Audio Track -> Track 2”. It seems odd, since we didn’t knowingly create two tracks.

Dave

sorry, here’s the attachment…
BF_id_cellsPIPE.mat (1.02 KB)

thanks guys we’ll give this a try!