diff --git a/README.md b/README.md index d408a04fa07b262b94d0d7efaec9d80906f07496..5431d24929ac5221fd30e8c3d784cedd5471c394 100644 --- a/README.md +++ b/README.md @@ -58,6 +58,7 @@ The algorithm has three parts: 3. Iteratively remove the peaks, starting from the highest. For each peak in that ordered set (starting with the one with largest gradient), check if it's still a peak, and if so, set the pixel value to the average of its neighbours. This had to be done iteratively because with high peaks, its neighbours can also be flagged as peaks, as their local gradient is influenced by the peak. The illustration below shows this in one dimension. With this iterative process, the central pixel (the real peak) is filtered, so when we next look at the neighbours, their local gradient is no longer above `diffth`, and are therefore no touched.  + *Illustration of the need for an iterative process to remove the peaks. The left graph shows pixels values in a one-dimensional image, along a line, with a high peak in the centre. The right graph shows the local gradients, while the dotted line shows the threshold `diffth`, meaning that the neighbours of the peak are also flagged as peaks.* This method is optimal in the sense that is modifies the minimum amount of pixels values (compared to a blunt filter like a median). @@ -86,6 +87,10 @@ These functions take as inputs the field and output filename. Saves to Portable Network Graphics format. In this format, the values have to be rescaled to the range `[0;255]` and converted to unsigned 8-bit values. + + +*Data saved as PNGs with this function, before (left) and after (right) processing. The black zones in the left image are the undefined pixel regions. Also, the left image seems much darker because of the rescaling: the peaks reach much higher values, so when bringing the value range down to `[0;255]`, all the useful values are squished in the darker greylevels.* + #### `save_Avizo_ASCII` Saves to an [Avizo](www.thermofisher.com/us/en/home/electron-microscopy/products/software-em-3d-vis/avizo-software.html) Ascii format. The advantage of this format is that no conversion is needed, the real values are conserved.