I’m trying to use Cellprofiler to count cells in a hemocytometer grid. I have a very simple pipeline to count cells in a regular microscope slide but when I use it to count the cells in the hemocytometer it doesn’t work because the program gets ‘confused’ with the hemocytometer grid, I think. Do you know how I can do this analysis? Another issue is the cropping of the image. I always image 12 squares of the grid and count the cells within the squares but all the images also include the borders of the neighboring squares and I need to crop that because I don’t want to count the cells in that region. The Cellprofiler manual recommends using the IdentifyPrimAutomatic module to find the boundary (they use the example of a plastic plate) and then a Crop module to remove the area of the image that you don’t want to use. I couldn’t get the IdentifyPrimAutomatic module to identify my area of interest so for the analysis I have been using already cropped images that only include the 12 squares of the grid. If you can give me some guidance as to how to create a pipeline for this analysis, I would really appreciate it. I put a sample image in picasa:
picasaweb.google.com/ferdyluly/C … cytometer#
Attached is a pipeline that may do the trick. The cells are found first from the color image and then a few tricks are performed to identify the grid sufficiently that DefineGrid can work. While it works for the nicely aligned hemocytometer image (IM0025), it fails for the skewed image, so when you take your images, make sure that the grid lines are aligned with the image border.
2009_06_10_PIPE.mat (1.91 KB)
When I opened the pipeline I got a message saying that the settings contained in the file were based on an old version of the ExportToExcel, ImageMath, SmoothOrEnhance, and LoadImages modules and that the settings might no longer be reasonable. When I tried to run the pipeline, there was a problem in the second module (ColorToGray) because it was expecting a file that hadn’t been created. However, when I looked at the settings of the ColorToGray module they look OK and the file that has to be used by this module was created in the LoadImages module. Any help on this? Thanks a lot!!!
Try downloading the latest version of CellProfiler from our website; we just released a new version this week. I believe I created the pipeline with this new release.
i was wondering whether i could i have the pipeline for your very simple method of counting cells in a hemocytometer? i’ve tried adjusting the grid system one but can’t get it to work i’m new to cell profiler. i’m counting cells on mylar so have no grtids to worry about