Rank: 3241 based on 15 downloads (last 30 days) and 1 file submitted
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TIAN ZHOU

E-mail
Company/University
DARTMOUTH COLLEGE

Personal Profile:

4th year PHD student in biomedical engineering at Dartmouth College. 8+ yr Matlab programming experience.

Professional Interests:
medical image processing

 

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Files Posted by TIAN
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05 Mar 2010 Screenshot Neuron counting Count the number of fluorescent cells (tagged with GFP) on noisy background fluorescence Author: TIAN ZHOU cell counting, cell number, cell count, biotech, gfp, neuron counting 15 5
Comments and Ratings by TIAN View all
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29 Mar 2010 ploterr plots data with x and/or y error bars and supports logarithmic scaling for both axes. Author: Felix Zoergiebel

13 Mar 2010 Neuron counting Count the number of fluorescent cells (tagged with GFP) on noisy background fluorescence Author: TIAN ZHOU

have you tried distance transformation before WST? there is a Matlab function BWout=bwdist(BWin).
i got this from my class notes by Prof. Alex Hartov
10 Mar 2010 Neuron counting Count the number of fluorescent cells (tagged with GFP) on noisy background fluorescence Author: TIAN ZHOU

hi, Rob
sorry for rating my own code. it is really not my purpose. i thought you have to click 'submit' for the rating to come out. and i haven't found a way to delete it.
you are right about the data type. it is really something i should consider.
the property of the slide bar can be changed in the GUI. select the slide bar, right click and select property inspector, and change the min and max value to expend the range. you might get an error when the threshold value is negative or more than one. i am not sure if it will help.
i'll also comment out the top hat part. i have a newer version GUI but don't want to upload it since it is really a minor change.

have you considered resizing your image before processing? enlarge them so each cell will have more pixel?
 
07 Mar 2010 shadedErrorBar Creates an attractive shaded error region rather than discrete bars. Author: Rob Campbell

05 Mar 2010 Neuron counting Count the number of fluorescent cells (tagged with GFP) on noisy background fluorescence Author: TIAN ZHOU

hi, Rob
thank you for the comments. that is what i am looking for.

i just uploaded a new GUI. hope you'll find it more user friendly.
to answer your question about the filtering parameter, it (i.e., the slide bar) changes the threshold values in the conversion from gray to BW.
if the bodies are touching, maybe the following link is useful to you
http://www.mathworks.com/products/demos/image/watershed/ipexwatershed.html

thank you

Comments and Ratings on TIAN's Files View all
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Updated File Comment by Comments Rating
13 Mar 2010 Neuron counting Count the number of fluorescent cells (tagged with GFP) on noisy background fluorescence Author: TIAN ZHOU ZHOU, TIAN

have you tried distance transformation before WST? there is a Matlab function BWout=bwdist(BWin).
i got this from my class notes by Prof. Alex Hartov
10 Mar 2010 Neuron counting Count the number of fluorescent cells (tagged with GFP) on noisy background fluorescence Author: TIAN ZHOU ZHOU, TIAN

hi, Rob
sorry for rating my own code. it is really not my purpose. i thought you have to click 'submit' for the rating to come out. and i haven't found a way to delete it.
you are right about the data type. it is really something i should consider.
the property of the slide bar can be changed in the GUI. select the slide bar, right click and select property inspector, and change the min and max value to expend the range. you might get an error when the threshold value is negative or more than one. i am not sure if it will help.
i'll also comment out the top hat part. i have a newer version GUI but don't want to upload it since it is really a minor change.

have you considered resizing your image before processing? enlarge them so each cell will have more pixel?
 
10 Mar 2010 Neuron counting Count the number of fluorescent cells (tagged with GFP) on noisy background fluorescence Author: TIAN ZHOU Campbell, Rob

Thanks, I had looked at that link in the past. My problem is rather difficult because the cell bodies as small so I have few pixels to work with. Although they are touching, the pears are fairly easy to isolate because each pear is composed of a large number of pixels.

Your new GUI isn't working for me. It doesn't check whether the input is of the right type. e.g. my image was an int8 and under those circumstances the threshold slider doesn't work. I edited the code to convert the image to a double after loading but then something else broke.

You will find other users of this site consider it bad form for an author to rate their own submissions.

05 Mar 2010 Neuron counting Count the number of fluorescent cells (tagged with GFP) on noisy background fluorescence Author: TIAN ZHOU ZHOU, TIAN

hi, Rob
thank you for the comments. that is what i am looking for.

i just uploaded a new GUI. hope you'll find it more user friendly.
to answer your question about the filtering parameter, it (i.e., the slide bar) changes the threshold values in the conversion from gray to BW.
if the bodies are touching, maybe the following link is useful to you
http://www.mathworks.com/products/demos/image/watershed/ipexwatershed.html

thank you

05 Mar 2010 Neuron counting Count the number of fluorescent cells (tagged with GFP) on noisy background fluorescence Author: TIAN ZHOU Campbell, Rob

Useful if cells are well separated but won't work for images were many cell bodies are touching. This problem is, naturally, difficult to solve.

GUI not particularly user friendly since it isn't obvious that buttons need to be pressed in a particular order. I can't see how filtering parameters can be changed from within the GUI.

Top Tags Applied by TIAN
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biotech, cell count, cell counting, cell number, gfp
Files Tagged by TIAN
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05 Mar 2010 Screenshot Neuron counting Count the number of fluorescent cells (tagged with GFP) on noisy background fluorescence Author: TIAN ZHOU cell counting, cell number, cell count, biotech, gfp, neuron counting 15 5

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