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A python tool for automated cell counting
Installation and quick start guide
SimpylCellCounter (SCC) provides an easy, fast, and reliable method for automatically counting cells in bright-field and fluorescent images as well as identifying co-expressing cells across multiple fluorescent channels. SCC serves as an algorithmically consistent method for quantifying images of cells, and its graphical user interface (GUI) is designed for ease of use.
Under the hood SCC uses OpenCV (Open Source Computer Vision Library) to separate out cell-sized, contrasted regions of images which are then filtered by size and degree of circularity. Cell counts per image, as well as various other image and cell properties are compiled neatly into a .csv file which can be opened with a spreadsheet editor. If counting cells for co-expression, the location of each cell will be stored in a .npz file which can be used along side other such files to identify cells that appear on multiple fluorescent channels.
SCC is known to be compatible with Windows and Mac systems, and Linux compatibility will be tested soon.