I installed Color Pixel Counter but it seems not to work. Independently of the image or the area or the color, the results is always “20 cells”… I doing something wrong… Thanks for help…
According to the documentation of the Color Pixel Counter plugin:
This plugin counts the number of pixels on an image (or selection) of a specified color. The pixel count can be converted to an object count (i.e. number of particles). The user can also input the number of cells on the image (or selection) and choose which results to display on a results table.
So I think - you as the user - decides how many cells are in the image… then the pixels/particles are counted within. However note - the plugin docs also say:
Select a region of interest to count. If no region is selected, the plugin will count over the entire image.
So in your case… the pixels/particles are being counted over the entire image.
This plugin is not counting your cells for you… they appear to want that as input.
Obviously, you’re right. Do you know any plugin, which facilitate the counting of cells?
Not necessarily a set plugin/tool… but you can segment your cells. Convert your images to 8-bit… and then you can follow a typical segmentation scheme in ImageJ. Check out our workshop (and updated slides) on Segmenting in Fiji (there is a nice example starting at 1:39:06). You can also look at the Segmentation page of the ImageJ Wiki.