I want to process an image stack such that every pixel with a color value below, say, 2000 is changed to a color value of 10000. What is the simplest way to do this?
You can do that by simply playing with the minimum and maximum intensity values using the Brightness & Contrast tool (Image > Adjust > Brightness/Contrast…). Just keep in mind that the changes won’t be done until your press “Apply”.
you can do in a manual way the following steps, I am using th dot_blot.jpg example image that you can find in File>Open Samples…
Use Threshold Tool (Image > Adjust > Threshold…) with Over/Under option so you can see in blue all the values below a certain value (in my case 100)
then from Edit>Selection>Create Selection you can create a selection, pay attention that you have also to invert it (this because usually the over/under option would exclude the blue areas: you can do it with Edit>Selection>Make Inverse
Finally you can the blue areas (the pixel with an intensity lower than 100) to a new value (in my case I decided for 255) with Process>Math>Set…
There is also a more programmatic way to do it, but maybe for you that could be enough.
Have a nice day,
In Fiji, there is also a convenient “Replace Value” command in “Plugins/Process”, but sadly, it works on 8-bit images only. Would be a nice feature to have it for all types…