The Threshold Smoothing Scale is used to reduce jaggedness and possible holes in identified objects. It is possible to adjust this parameter so all the bins are the same size across cells, but it will mean that small cells might not have all bins or that the number of bins won’t completely cover larger cells. Once the nuclei of all the cells in an image are identified as primary objects, CellProfiler can identify the cell bodies surrounding each nucleus as secondary objects. In this article, MitoTracker Orange will be referred to as MitoHealth. Because you are using “Membrana_basada_en_acTub” as the objects in these measurements, it will be in the text file with that name.Īs you have it set up for the module, the widths for each bin are being normalized per cell (depending on the cell size). We subsequently use a CellProfiler image analysis pipeline to quantify intracellular mitochondrial fragmentation and fluorescence intensity of mitochondria in the peri-nuclear area of SN4741 neurons (see Basic Protocol 2 ). The ExportToSpreadsheet module exports the values for each cell at the different bins at the end of your analysis run as a text file.
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