Need help or advice ? Come to the Icy club ! - Every other Thursday morning from 9h30 to 12h30 - Francois Jacob Building - Main hall - Pasteur

User reviews

5 star
4 star
3 star
2 star
1 star
average rating: 2.67

Please log-in to post a review
27 Apr 2017 13:50
When objects of interest are small, the ROI detect label can mask some of them. There should be an option to display only the marker.
As said below, it would be better to have the counts in a separate window, here again to avoid masking part of the image.
After testing Spot Detector, it would be nice to be able to run it on a given image, and then use Manual Counting to pick up the missed objects, and clean up the false positives.

After trying Spot Detector on immuno images, the resu
University of Vienna MFPL
13 Oct 2016 11:16
Nice counter, but it would be nice to have the counts in a separate window. Also, it would be nice to be able to save the counting data to an excel sheet. Finally, I can't figure out how to turn off the counting once I've started. Maybe there could be a window with stop/start/reset and save buttons?
22 Dec 2015 16:12
It is a great plugin but some functions miss.
I am 100% sure to convince biologists to use ICY when "Counting Manual" will have exactly the same functionalities as the ImageJ / Fiji "Cell Counter".
16 Oct 2015 18:27
A very handy plugin! I would really like a simple reset button to clear the counter and start over. Individual counter numbers for each color of marker would be a nice addition as well.
29 Sep 2015 17:19
For 2D is fantastic! Great tool!
Alexandre Dufour
24 Jun 2014 17:58
great but does not keep Z info ;)

Manual Counting

by Fabrice de Chaumont

Interactive counter.
Click on the sequence to add detection, see number of detection in ROIs directly over the sequence.

Publication Id
See technical details
View complete changelog


This plugin is an helper, designed to help you counting objects that we can't find automaticaly

  • To add a point, just click where you want to create the detection. This will be a ROI named 'detect'
  • To remove a point, right click on it.

On the sequence, you will see in the hand top-left corner:

  • Total number of detection
  • And for each ROI, its surface in pixels and in scaled unit. (micrometer, millimeters...), and the number of detection contained in it.