Problems with cell detection and processing

[thiago...@gmail.com]

Hi,

(1) MicrobeTracker is only detecting ghost cells in my images. I've tried increasing threshFactorM, but nothing changes. Segmentation is always the same regardless of the threshFactorM I use. 

(2) For some other images, when I try to join cells, I get the following error:

Subscript indices must either be real positive integers or logicals.

Error in microbeTracker>graythreshreg (line 7320)

        res = graythresh2(img(ceil(sz(1)*0.05):floor(sz(1)*0.95),ceil(sz(2)*0.05):floor(sz(2)*0.95),1));

Error in microbeTracker>forcejoincells (line 6746)

    thres = graythreshreg(imge,p.threshminlevel);

Error in microbeTracker/manual_cbk (line 1910)

        lst = forcejoincells(frame,selectedList);

 

Error while evaluating UIControl Callback

Any suggestions on how to fix these problems?

Thanks,

T

[Bryant Walker]

What are you using during imaging of your cells? Because I have had the same problem when using microfluidic chips with channels. This problem for us came from phase images that are not as good because of the index of refraction of the PDMS that we use in the chips so our phase images are not as good so microbeTracker creates ghost contours and then has trouble finding boundaries for other cells? Other wise using LB or M9 pads we have had no issues with the program detecting the cells. Make sure you are using the correct parameters and that your images are preferably TIF images.