Disappearing multi-point counters

Hi. I’m very new to ImageJ/FIJI, so getting a bit frustrated with it and my limited knowledge. I’m counting items in a very large file (1.4Gb TIFF). I have successfully applied 639 numbered counters with the multi-point tool to the items I’m looking for and saved a TIFF copy. This opens nicely in FIJI and allows me to zoom in (with +) and move around with ‘Space bar+ mouse/left click’. All well and good, but after a short time and for seemingly no reason, the numbers disappear as I click the space bar/click to move. I’ve tried a few random ideas involving overlays and ROIs, but nothing seems to get my number overlay back. So I have to close and reopen and start again, until they disappear again.
I have been careful not to press Alt, or anything other than shift to move around the image. Is there any way that I should be moving the image around that might not eliminate my numbers? Or is there a simple sequence of keys that will restore them? I like to think I’m missing something really simple and obvious here. Many thanks for any suggestions.

Hi @PaulSST,

I don’t have a solution for this multi-point roi trouble, but I can recommend you to have a look to the Cell Counter plugin.
You can have several counters, it works in 3D, you can save pointers in an xml file and reload them later.



OK. Thanks. I’ll have a play. I have subsequently realised a simple solution to the space bar/click issue, in that I can just use the hand tool for moving around, so perhaps my numbers may not disappear now…However it would be good to know why that was happening, as it is a much quicker way of getting around the screen. The XML file of the points sounds really useful. I’ll give it a go. Cheers.

That sounds a bit backwards to me: on several places here on the forum, it was recommended to use the (built-in) multi-point tool instead of the (poorly-maintained) Cell Counter, and also on the official documentation page, it says:

:information_source: Please consider using the built-in Multi-Point Tool in ImageJ, as this tool now replicates most of the functionality of Cell Counter.

Let’s try to fix the issues together, and work on implementing any missing features that are present in Cell Counter but not (yet) with the multi-point tool. We need community effort that starts with pointing out where things are going wrong, so thanks for the report in the first place @PaulSST!

Sorry :sweat_smile: please forget what I wrote then, I didn’t know about these recommendations (should come more often)

@imagejan can you add a link with tuto of the new functionalities?
I’m particularly interested by adding/removing single point from a category (here I guess it would be a set of multi-point).



I’m afraid there’s not much more than the paragraph in the user guide, but as written there (for both the Point and Multi-point tool actually), press Alt to remove any single marker.

Oh, and double-click the multi-point tool to get the dialog for counter selection etc., in case that wasn’t mentioned yet. :slight_smile:

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ImageJ 1.52c or later is supposed to display the following dialog box before deleting a multi-point selection with more than 10 points. Do you see this dialog? It would help if you could post a TIFF with a multi-point selection that we can use to reproduce this problem.


Hi Wayne. No I don’t get any dialog, they just disappear. To be honest I don’t know how to post a sample of my images and they are far to big to upload in their entirety (29,000 pixels wide). I can well imagine that the problem may be due to this size.They also comprise of 2 channels, a brightfield version and a fluorescent version, which, again, may be unusual and problematic. Now that I am using the hand tool to move around, I am not having the same problem.
After completing my current task, using the hand tool to move, I reverted to using the space bar method as a test and of course it isn’t causing a problem any more! It’s all working perfectly well. Although it takes a moment longer to switch tools, rather than using the space bar, I will continue with this method, despite that no longer seeming to be a problem (I don’t quite trust it…). Thanks for all the advice from everyone. Sorry it has been a bit of a waste of your time. It is currently doing the job beautifully.

Upgrade to the latest ImageJ daily build (1.52p57) and you should not have this problem. Now, when you click on an image with markers, and you are not using the multi-point tool, you get this dialog:

And if you use a command like Select All, that would have previously removed the markers, you get this dialog:

Both dialogs have “Help” buttons that displays this window:

Thanks. I did notice this dialog yesterday. The restore selection tip was very helpful. All seems OK now. Cheers.