Problem with multi-point tool: switches counter measurments to generic x-y coordinates

Hello everyone,
I am experiencing a problem with the multi-point tool. I have a stack with 3 channels and several slices and I have to manually annotated different features with the multi-point tool. It has occured several times that during the analysis, all the different counts (4 to 5 types) would turn to one generic x-y coordinate type. This is quite frustrating as I have to annotate up to 500 points per image.
Trying to reset the selection through “Edit > Selection > Restore selection” was of no help: all points are converted to counter 0 type…

I am currently using the version 2.1.0/1.53h of FiJI.
Has anyone experienced something similar and/or knows how to solve this?
I would be so thankful!


Hi @ananahana,

Are you using the Image>Overlay>Flatten command (shortcut=shift+f)? The latest ImageJ daily build (1.53i8) fixes a bug where this command caused multi-point selections on stacks and hyperstacks to lose counter information.

Thanks for the reply @Wayne.
No I don’t use the Flatten option.
Since then I noticed that the problem occurs in the following occasions:

  • when during the quantification you switch through channels
  • when you try to change brightness and contrast of the stack
  • sometimes for no apparent reason :smiley:

I am now on the version 1.53c and can’t see the option of 1.53i8 on my Mac.

To upgrade to the ImageJ daily build, use the Help>Update ImageJ command and select “daily build” from the drop down menu.

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