Also, maybe I should create a new topic for this, but I was just wondering, is there a way to measure fungal colony density using Cellprofiler?

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Unfortunately, no. CellProfiler is intended to be units-agnostic, so any further conversions will need to be done downstream with 3rd-party software, e.g., Excel and the like. -Mark

I am having problem figuring out how to convert pixel unit to mm. For my experiment, I take pictures of fungal colony plates using a digital camera at 5 megapix. Then, I load the images into CellProfiler to analyze the morphology of the culture. I am really obtuse at figuring out stuff like this, but I wonder if it’s possible to convert pixel to mm directly, as in, 1 megapixel = 0.264 mm, or is there a certain procedure that I need to go through to work out the conversion constant?

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Although there are several unit converter websites for converting pixel to mm, but I guess it’s not as simple as that, i.e for the same image taken at two different digital camera resolutions, we will find that at a given area, it will show two different pixel values.

Then again,I wonder how CellProfiler treats and measures the images loaded? Would difference in image resolution produce different measurements? I figure, by understanding this, I would be able to find out the conversion factor.

I know this post was answered a few years ago, but I’m struggling with a related part. I want to calculate areas based on the scaling factor I put for pixels to mm. I did put the scaling factor to scaling in the CalculateMath module, but any posterior measurement just takes the # of pixels as distance. I was not able to call this scaling factor in other modules to measure the area or other parameters. Any alternative?

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As for the first question, I’m still struggling with the problem: CalculateMath can solve the problem provided that I know the conversion factor. However, I am having trouble figuring out the conversion factor to convert the measurements generated from CellProfiler in pixel unit to the physical mm unit. Although there are several unit converter websites for converting pixel to mm, but I guess it’s not as simple as that, i.e for the same image taken at two different digital camera resolutions, we will find that at a given area, it will show two different pixel values.

I am having problem figuring out how to convert pixel unit to mm. For my experiment, I take pictures of C.heterostrophus colony plates using a digital camera at 5 megapix. Then, I load the images into Cellprofiler to analyze the morphology of the culture. I am really obtuse at figuring out stuff like this, but I wonder if it’s possible to convert pixel to mm directly, as in, 1 megapixel = 0.264 mm, or is there a certain procedure that I need to go through to work out the conversion constant?

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Correct, the scaling will depend on the optics involved (the various filters, objectives, lenses, etc). The typical approach is to use a stage micrometer (described here); you can google for more references. You would take a image of the micrometer with the same acquisition settings as your sample and get your conversion factor from that.

I would recommend using the CalculateMath module and select the measurement you want to convert, None as the operation, and enter the conversion factor under “Multiply the above operand by.” Of course, you can only do this for one measurement at a time.

Also, maybe I should create a new topic for this, but I was just wondering, is there a way to measure fungal colony density using CellProfiler?