Rat Neocortex. Cell count. How to select multiple dots at the same time. Help

I have used the cell counter plug-in that comes preinstalled with ImageJ to count cells on a micro photograph. After placing many markers (dots), i would like to select an area and know how many markers (dots) there are in that area (Here’s a picture of what i mean. http://imgur.com/a/0VlTF). However, the dots seem to disappear whenever i use the “freehand selections” tool. Is there a way to select only the first box and make imageJ count markers in that selected area?
I know that the dots have a number attached to them but i recently went back added more dots. and since the dots are sequential i cant really know for sure how many there are in one single box.
Thank you

In the Cell Counter plugin you can select type 1 for the first box and type 2 for the next box and so on.
Then select “Measure” and you get the counts for each type (in your case the box).

However if you have only one type you can also use the default Multi-point tool and add a multipoint object (your rectangle) to the ROI Manager which persists if you make a new selection. Then measure the different multipoints.

If you want to count some cells automatically try to use the Particle Analyzer on a rectangular selection (threshold the image or use the Trainable Weka segmentation plugin to mark the cells)

Hello Bio7,

First, thank you for the response. Im completely new to ImageJ and im having a hard time using ROI manager to count cells in my selected “box.” All i managed to do is add my dots to the menu. then add a new rectangle (in order to select the cells i wish to count). but then i have no idea what to do next. i tried going to measure but nothing happens. :frowning:

Any chance you could take a crack at it? I have a dropbox link where you can download my image (in .tif format). https://www.dropbox.com/s/5o137tdyxml95vm/CC%2014%20slide%205%20slice%202%20L3%20100x__1473540288_96.236.70.168.tif?dl=0

I tried to upload it here but the system wont recognize it.

Please and thank you.

Ok you have already an image with multipoint selections. You can add them to the ROI Manager by selecting a Point and pressing the ‘t’ key.

However you cannot split a multipoint object (as far as I know).

With a trick you can get the positions again and then measure the single rectangle selections.

  1. Press ‘t’ (Edit->Selection->Add to Manager) to add the multipoint object to the ROI Manager.

  2. Duplicate the image (Image->Duplicate)

  3. Enable the same ROI in the Roi Manager for the duplicated image (which should be selected)

  4. Select a point and press ‘d’ (Edit->Draw) which draws one black pixel (or any other selected color you like) at each point.

  5. Remove the multipoint selection by using ‘Select none’ (Ctrl+Shift+A) or simply click in the image to remove them.

  6. Convert the duplicate to a greyscale image

  7. Threshold the image (Image->Adjust->Threshold) to select the black drawn pixels only (see image below)

  8. Create you rectangular selection around the points

  9. Then Analyze->Analyze particles (select the option “Add to Manager”), see below.

The points will be added to the ROI manager which you can then enable again on the original image to make you measurements on the original image (select all ROI’s with Ctrl+click or Shift+click and then Measure).

Apropos you can use Edit->Selection->Restore Selection if you want to see a hidden selection again (if you have by chance clicked into the image).

And of course you can write a macro to seperate the points according to the x- and y-coordinate if you want learn more about ImageJ.

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