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Fluorescent data
PMA.core supports various fluorescent file formats. To get a list of most recent supported formats, have a look at https://www.pathomation.com/formats.
Histogram clipping
The software offers the option to clip a fluorescent channel within a range of intensity values (min/max). In other software, this range is typically set to the pixel depth of the image (8, 16 bits etc.). Other times it is set to the actual min & max values within the pixel data of the image. Our approach is kinda mixed. We only allow the user to clip between the range 0 to 100, as a normalized range, regardless of the underlying format.
Note that our range doesn’t always refer to the same range. If the underlying image has 8-bit pixel depth, it is mapped to 0-255. If the bit depth is 16 bits, it is mapped to 0-65K. However, if the image defines a min/max range, then it is mapped to that range. There are many file formats that have attributes which dictate the actual intensity range, in order to improve the conversion accuracy from 16-bit to 8-bit.
