![]() Example images and CellProfiler outlines for these cell types are shown in Figure 1e. For images of Drosophila Kc167 cells with various genes knocked down by RNAi (right), the two researchers' counts varied by 16% and CellProfiler's counts were within 17% of their average. (a) Cell count: for a set of 6 images of wild-type human HT29 cells (left), two researchers' counts varied by 11%, and CellProfiler's counts were within 6% of their average. Validation of CellProfiler for many cellular phenotypes. Cells touching the border are intentionally excluded from analysis and images were contrast stretched for display. (e) Outlines show the identification of nuclei and identification of cell edges made by CellProfiler in human HT29 (left) and Drosophila Kc167 (right) cells. The results are comparable to those produced by white referenced images (right), but they do not require the error prone and often omitted step of collecting a white reference image immediately before image acquisition. (d) These corrections reduce noise in quantitative measurements, demonstrated here in DNA content measures (middle) from images of Drosophila Kc167 cells that are improved over the raw images (left). Images were contrast-enhanced to display this effect. CellProfiler's illumination correction modules correct these anomalies (right). (c) Image processing example: uneven illumination from the left to the right within each field of view is noticeable in this three row by five column tiled image (left). (b) Schematic of a typical CellProfiler pipeline. (a) Main CellProfiler interface, with an analysis pipeline displayed. Now the pipeline halts, but there is no error popup.CellProfiler overview and features. Make it run again without changing anything: enter Test Mode and click Run. "Stop Processing." but being a silly user, I just try and see if I can The error should direct the user to NamesAndTypes.Īlso there is another issue with the exception popup. ![]() User gets when converting an old pipeline, but regardless I suggest that Grayscale instead of color, but the naive user will not know this.Įspecially since I have had this happen to old, converted pipelines thatĭon't set the image type automatically. The problem is (of course?) NamesAndTypes having "Select the image type" = I load what is (really!) a color image,īut then I run Test Mode on it and get this message, telling me it is On Thu, at 11:56 AM, David Logan have had this happen to me at least twice and I have thought "But wait, Mode, also reasonable not to - I can keep as is or change. It seems reasonable to clear the list when starting test Currently, this happens when you load a pipeline and when you start a On the other hand, you'd like any major action to clear this ![]() Throws an exception every time it refreshes in which case you can't get out You want to avoid being endlessly annoyed by the errorĭialog while you're trying to recover from it (most notably, if the UI Regarding the window not popping up, there's some code in CP to ignore In some cases, the output image color/gray flavor will depend on the input Information and every module that outputs an image give this information. You'll have to make every module that inputs an image understand this It's a slightly ambitious undertaking because Of image provider and subscriber so that you would only be able to selectĬolor images in ColorToGray. My long-term plan is to add information about the image type to the flavor Here's a misconfigured project file and a color image: The console shows the error but there is no popup. Now the pipeline halts, but there is no error popup. I then click "Stop Processing." but being a silly user, I just try and see if I can make it run again without changing anything: enter Test Mode and click Run. Yes, it is in the long text box the user gets when converting an old pipeline, but regardless I suggest that the error should direct the user to NamesAndTypes.Īlso there is another issue with the exception popup. Especially since I have had this happen to old, converted pipelines that don't set the image type automatically. The problem is (of course?) NamesAndTypes having "Select the image type" = grayscale instead of color, but the naive user will not know this. I load what is (really!) a color image, but then I run Test Mode on it and get this message, telling me it is grayscale: ![]() I have had this happen to me at least twice and I have thought "But wait, my image is color?" both times. ![]()
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