Counting coloured images

[wiggs 38]

Hi,

I have images which have numerous brown dots which I want to count, I am able to use the color threshold picker to create a mask that selects only the brown dots and excludes the purple stained tissue. Is there a way to count each particle in the mask?

Thanks Icy community!!
George

[Stephane]

Hi George,

Did you test the Spot Detector ? I think that is the plugin which suit your needs :)

Best,

- Stephane

[wiggs 38]

Hi Stephane,

I have attached an image so you can better see what I am trying to achieve. Basically I want to either count the total numbers of brown (DAB) dots or the number of cells with a brown dot. The first is going to be easier and I have managed to achieve this by doing both the color threshold picker and then saving the mask as an image, this then allows me to use the spot detector.

The only problem is I can't seem to use the color picker threshold for a batch of images or incorporate that into a protocol or save the colors that I used for creating the mask. I am therefore left to do every image (with different color palettes ) , save the mask then do batch spot detection.

Can you think of a better solution? - I am very new to bioimaging, might be something obvious I am missing.

Thanks you

George

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Regards,

George Wiggins

[Stephane]

Hi George,

Thanks for providing an image so i can test. Indeed the image really require you to use the color threshold picker as you already did. And unfortunately the Color Picker is not compatible with protocols (it's a old plugin and the author is not working anymore on it). We will try to see if we can make it compatible with Protocols but in the meantime (as it won't be done before some months at best) you might try to use a script block inside the protocol which let you more access to Plugin in general, but even using script i have to admit i don't know how much you can automatize the process, specially if you need to use different color palette for each image. Sorry for not having better to propose..

Best,

- Stephane

Le lundi 18 juillet 2016 22:04:51 UTC+2, wiggs 38 a écrit :

Hi Stephane,

I have attached an image so you can better see what I am trying to achieve. Basically I want to either count the total numbers of brown (DAB) dots or the number of cells with a brown dot. The first is going to be easier and I have managed to achieve this by doing both the color threshold picker and then saving the mask as an image, this then allows me to use the spot detector.

The only problem is I can't seem to use the color picker threshold for a batch of images or incorporate that into a protocol or save the colors that I used for creating the mask. I am therefore left to do every image (with different color palettes ) , save the mask then do batch spot detection.

Can you think of a better solution? - I am very new to bioimaging, might be something obvious I am missing.

Thanks you

George