Hi, I wonder if anyone can give me some tips. I'm a cell biologist, and a complete Bioinformatics noob.
I am growing some breast cancer cells that have a fluorescent protein in them that will fluctuate over time. I am taking photos using a time lapse fluorescence HD camera at 3h intervals. By eye I can easily see which cells are fluorescing, which are dividing, and also which cells on one image give rise to what cells on the second. However what I need is some software that will allow me to track each cell and each of its daughters and grand-daughters, etc and incorporate that data with the fluorescent intensity of each cell.
As I see it I have three issues:
(i) one of image classification, ie detecting the cell boundaries and fluorescence from each image (for which I'm using ilastik http://www.ilastik.org/ and it kinda works)
(ii) parent-daughter cell identification, ie marrying up a cell from one image to the next and to their daughters when a cell divides (note, I can also detect cell division events using ilastik)
(iii) exporting the data (.png files in this case) and constructing phylogenetic trees that will incorporate the fluorescence intensity data.
I can (sort of) tackle the first issue, however it's the second and third that I'm really struggling with. Some people have mentioned that I should be able to do it using ImageJ and some plug-ins, but I'm completely clueless about this.
Any help would be greatly appreciated.
Thanks in advance. Al
ps - attached is a sample image so you can see what I'm working with.
Thanks guys, these are both great suggestions. I'll be sure to give both a try.
kindest regards
Alasdair
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