Cell Counter Help

[Erica B-3]

Hello,

I downloaded the Cell Counter plug-in to count cells in an image that I've already filtered with the particle analysis tool. I'd like to count the particles without having to manually select each one. Could someone please explain how this works?

Thank you!

-Erica

[Citron, Bruce]

Erica- The Cell Counter plug in is for manual counting.  There is plenty of
documentation with the various particle counting capabilities of ImageJ
through the ImageJ site, but here is our abbreviated cheat sheet for cell
counting.
-Bruce
Bruce A. Citron, Ph.D., Dir., Lab of Molecular Biology,  Bay Pines VA
Healthcare System, Res. & Dev. 151


Cell Counting
I.         Software
A.       ImageJ
    1.        Obtain latest version from http://rsb.info.nih.gov/ij
        a.        Instructions were generated for version 1.38x
II.       Image Capture
A.       Collect micrograph and save as TIFF

B.       Work on a copy of the image, and as it is processed, save
intermediate versions

C.      May Downsample to reduce image size
    1.        Best if reduction is a factor of 2 or 4
        a.        Image-Scale
        b.       Will reduce image size as the square of the linear
reduction

D.       Optionally, Enhance signals in channels used
    1.        Image-Adjust-Color Balance
        a.        Red-Auto-Apply
    b.       Green-Auto-Apply
2.        Save Image as Tif

III.     Cell Counting
A.       Open image by dragging onto ImageJ icon
    1.        Set dimensions to actual dimensions using
        a.        Analyze- Set Scale
            i.          and measure a known distance or
    2.        Image-Properties
        a.        Set pixel size to actual pixel dimensions

B.       If color image
    1.        Image-Color-RGB Split
        a.        Will divide image into 3 separate images, one for each
color
        b.       Save desired greyscale
    2.        Image-Adjust-Threshold
        a.        Adjust Minimum and Maximum to just include desired cells
    3.        Close Threshold window

C.      Operating on RGB Image directly
    1.        Plugins-thresholdcolour-Threshold Colour
    2.        Select RGB at the bottom
    3.        Adjust thresholding for the color desired
    4.        Click Threshold to convert to binary

D.       Manual counting different types of cells
    1.        Plugins- Cell Counter
    2.        Set to desired type
    3.        Click away

E.       Counting Cells automatically
    1.        To separate cells in contact with each other
        a.        Process-Binary-Make Binary
            i.          All three boxes checked
        b.       Process-Binary-Watershed
    2.        Analyze-Set Measurements
        a.        Area
        b.       Min & Max Gray Value
        c.         Center of Mass
            i.          Location of Cell
        d.        Mean Gray Value
            i.          Mean intensity of cell
    3.        Analyze-Analyze Particles- selecting
        a.        Display Results
        b.       Clear Results
        c.         Summarize
            i.          May adjust size range that will count
            ii.         May adjust circularity to count
                1)       Circularity=4parea/perimeter2=1.0 for perfect
circle
            iii.        May exclude any cells touching the edge of the image
area
        d.        May Show Outlines of counted cells

F.        Placing the cell outlines and numbers on the original image
    1.        Reopen the last RGB image
    2.        Image-Color-RGB Split
    3.        Select the Outline Drawing window
    4.        Edit-Invert
    5.        Plugins-RGB Gray Merge
    6.        Select the following images for the Stacks:
        a.        Gray- Drawing
        b.       Red- (red) split
        c.         Green- (green) split
        d.        Blue- (blue) split
        e.        May Keep source stacks; OK



On 11/25/07 11:48 , "Erica B" <[hidden email]> wrote:

> Hello,
>
> I downloaded the Cell Counter plug-in to count cells in an image that I've
> already filtered with the particle analysis tool. I'd like to count the
> particles without having to manually select each one. Could someone please
> explain how this works?
>
> Thank you!
>
> -Erica