I used the record function to produce a macro that counts cells in multichannel confocal images. However, the macro returns a zero for the cell count for an image that produces a count of 550 when I run the same set of commands by hand. Any ideas why this is happening?
The macro produced by the recording is:
run("Make Binary", "method=Yen background=Light only black"); run("Despeckle", "slice"); run("Analyze Particles...", "size=5.22-22.00 display clear include summarize slice");
The action that I am doing by hand: Proces -> Binary-> Make Binary ( Method: Yen, Background: Light, Black background, only convert current image.
Process-> Noise-> Despeckle
Analyze-> Analyze particle