I’m one new user of cellprofiler . I want check megakaryocytes polyploïdization by Cellprofiler as it’s shown in the Brochure of cellprofiler. I’ve found aussi there is one publication (Qiang Wen et al. Cell 2012) which used Cellprofiler to measure DNA content of megakaryocytes. Is there some people could tell me if there exists already one pipeline for this kind of analysis?
Thanks a lot
The pipeline we used for this paper was actually fairly straightforward. All it did was identify the nuclei using IdentifyPrimaryObjects, measure the intensity using MeasureObjectIntensity and save the results using ExportToDatabase (or ExportToSpreadsheet if you’re not doing a full blown screen). Since the nuclei often clumped together (which can make identification difficult), we used MeasureObjectNeighbors to measure the amount of the cell border touching a neighbor for each cell, then use FilterObjects to remove all nuclei which had more than 60% of their border touching a neighbor.
However, the data analysis itself (shown in the plots in the brochure, as opposed to the image analysis) was done outside of CellProfiler, using scripts written in R. The relevant measure examined was the per-cell integrated intensity of the DNA channel (measured by MeasureObjectIntensity); the bulk of the analysis was determining the separation between control and treated cell populations, which is outside the scope of what a simple CellProfiler pipeline is capable of.