Differentiation Between Each Point For Click Based Instance Segmentation

[JB4Jaison]

Hello team!

First of all, amazing job on the napari plugin for SAM! Makes annotation tasks much simpler and my workload is almost halved as compared to previous workflows!

I had one concern though. Currently as I am performing instance segmentation using the click annotation mode, is it really difficult to discern which point is a positive click and which ones are negative. There are cases where two points are to be close to each other (such as boundaries) where one might be a positive one and the other one negative but, there is no way of confirming which one's which. One should currently rely on memory or going for a full-on undo streak till you reach that point. Is there a way of adding another color or shape for each point to differentiate between each click?

Also, a similar problem is when you have multiple labels in the same image. Every single click is a white dot which can cause similar problems as above.

[Karol-G]

Hey,

Thanks for noticing this problem! Usually, the points should be colored with the respective labels. However, at the moment points don't scale with the image size appropriately. So it might be that you are working with a relatively large image, which results in small white points. Could you maybe screenshot and upload an example image with points to confirm this issue? Could you also give me some exemplary image sizes you are working with?

In normal circumstances, the points should look like this:

Best,
Karol

[JB4Jaison]

An example image with the dots would be the one below:

Images sizes vary from 60MB to 130MB. They are 3D tiff files with around 300 images in a stack.

[Karol-G]

Have you tried to increase the point size? This might solve your problem.

[JB4Jaison]

I might need a bit more help on where these settings are located. I have tried changing the point size in the "Ignore this layer" layer but then it defaults to size 3 the next time I do a middle mouse click.

[Karol-G]

The point size options are on the napari-sam widget itself on the right sight below the activate button.

[JB4Jaison]

I had to update napari to see these options. Now that I did, I have tried changing the size and it seems to have no effect.

I have noticed that the point's face and edge colors are white on the "Ignore this layer1" layer. Is this supposed to automatically update to the color of the label? (I am using the same label color as in the previous image)