![]() ![]() The term SUM(pixel_values) is known as the Raw Integrated Density, and is independent of spatial calibration. ![]() So, the mean value of the spatially calibrated image results: mean = IntDen / A = ( SUM(pixel_values) * sf^2 ) / ( N * sf^2 ) = SUM(pixel_values) / NĪs you can see, you arrive at the same expression as before for the mean, regardless of the spatial calibration.Īlso note that the IntDen value does in fact depend on the spatial calibration. That is: IntDen = SUM (pixel_value * pixel_area) = SUM (pixel_value * sf^2 ) = SUM(pixel_value) * sf^2 The first term is called Integrated Density (IntDen), and is the sum of the contribution of each pixel weighted by its area. ![]() What happens if the image is spatially calibrated? Well, in that case, you can think of the mean value as the quotient of two magnitudes: a total value integrated over the whole image, divided by the area it represents. What is the mean value of the image? If the image is not spatially calibrated, you can calculate that quantity by summing the values of every pixel and dividing by N, which effectively yields an average pixel value: mean = SUM(pixel_values) / N So, the area of an image is simply the product: (In the case of no spatial calibration, sf = 1) 0.1 micron/px), then the area of a single pixel is sf * sf = sf^2. Now, if you know that these pixels are spaced by some magnitude sf (e.g. So, for example, if you have an 8-bit image, it is just a table of integer values ranging from 0 to 255.įor an image which is not spatially calibrated, the area is just the amount of pixels it contains. a function that maps raw pixel values to some other intensity scale: OD, temperature, etc.).Īlso, let’s remember that an image can be simply viewed as a table (rows and columns) composed of cells (pixels) that have some (finite) range of posible values. Let’s start by noting that there are two different types of calibration: spatial calibration (i.e. Hi issue is usually a source confusion to many users. if interpixel distance pixel in the image is scaled to 0.5 micrometers then IntDen=RawIntDen*0.25 sq um but it uses the same pixel brightness units (either calibrated or not). Thus Integrated density=Raw Integrated density * Area of a region with size one pixelĮ.g. Integrated density equals the Mean Grey value (or mean OD, or mean electron number etc) times the area in scaled units. Raw Integrated density is the sum of all pixel values (or ODU, etc) in an area, while the a scale is set (a physical distance unit is assigned to the interpixel distance ) the Integrated density is different from the Raw Integrated density in the already explained dependancy: If the image interpixel distance is calibrated,i.e. If the image brightness is calibrated both the mean grey value and the Integrated density are reported in calibrated units. For the calibration of the interpixel distance is used the term “image scale”. Optical Density units, photon number, electron number etc). ![]() In imagej “calibration” is the assignment of a physical meaning to the grey values of the pixels (e.g. The difference between Integrated density and Raw Integrated density is in image scaling and not in Calibration. ![]()
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