http://imagej.273.s1.nabble.com/Disector-counting-frame-tp3688237p3688240.html
> Dear Teresa,
> this an ingenious approach. I have some macro lines that prompt for user input regarding grid placement and will create the grid with a systematic random placement that I will send separately.
>
> Regards,
> Glen
> Glen MacDonald
> Core for Communication Research
> Virginia Merrill Bloedel Hearing Research Center
> Box 357923
> University of Washington
> Seattle, WA 98195-7923 USA
> (206) 616-4156
>
[hidden email]
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>
> On May 20, 2010, at 4:01 AM, Teresa W wrote:
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>> I used this approach to produce an unbiased dissector frame, and it may help
>> those searching under this topic. I recorded the process as a macro and ran
>> it automatically once I had determined the sizes of the different squares.
>> It can be run on individual images or on an image stack.
>>
>> Squares are defined in IJ by (X, Y, width, height), where XY is the
>> right-hand top vertex. A random number generator and a spreadsheet can be
>> used to calculate random XY co-ordinate start points, and so satisfy the
>> requiremnts of an unbiased dissector.
>>
>> Set on Record Macro to capture procedures.
>>
>> From your thresholded binary image, first sample a square around 2x the size
>> of the largest particle you want to count. Save as Sample image.
>>
>> Set the Scale to global. Create and name a square frame image of the same
>> size as the Sample square. Use New image & choose the required pixel size.
>> Draw a slightly smaller square inside and fill it to give a border of black
>> ~ 5-10 pixels. Save this border square as a binary Frame image.
>>
>> Within the Sample image, draw a Count square to a known size (e.g. 1 mm2),
>> starting from 0, 0 of the Sample image. Run Analyse Particles, Include On
>> edges, Show Masks. Save the Mask as a binary Mask1 image. Save all Mask
>> image as binary images, or later Image Calculator functions may not work.
>>
>> Return to Sample image and use the Polygon tool to create an L-shaped ROI
>> the inverse of the Count square, which shares 3 common vertices with the
>> Count square on the inside part of the L. Using this L-ROI run Analyse
>> Particles, Include On edges, Show Masks. Save Mask as Mask2 image. Then run
>> Analyse Particles, exclude On Edges, Show Masks. Save Mask as Mask3.
>> Subtract Mask 3 from Mask 2 to get only the particles intersecting the edges
>> of the L-shaped ROI. Save as Mask 2. Add Mask2 to Mask1, Add Frame. Save as
>> Mask2 and run Analyse Particles, exclude On Edges, Show Masks.
>>
>> This gives you an image or a stack where the top and right-hand particles
>> touching the Count square are excluded, while those jutting out of the
>> bottom and left-hand have been stitched onto edges and are counted. There
>> can be problems if your particles are too large for the Sample square and
>> are truncated when they hit the border resulting from the Frame.
>>
>> For stacks, I found that large stacks work best where the image stacks are
>> all saved onto the Desktop, the use of Create New Window is used only when
>> necessary, and intermediate image stacks are saved (hence all the Save
>> steps).
>>
>> Teresa Wegrzyn
>> Institute of Food, Nutrition and Human Health
>> Massey University
>> Palmerston North New Zealand.
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>> --
>> View this message in context:
http://imagej.588099.n2.nabble.com/Disector-counting-frame-tp636956p5079117.html>> Sent from the ImageJ mailing list archive at Nabble.com.
>>
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