![]() This method certainly isn’t ideal since the module requires several seconds to calculate, which for a large, 3D dataset may add a significant amount of time to the computation “Method to draw dividing lines between clumped objects” → Intensity.Set “Method to distinguish clumped objects” → Intensity.The most relevant settings from the screenshot below are: While I couldn’t find a good example image of my own that has adjacent objects to test this, here is an example image as well as the settings that could be used. Since the intensity is based on the objectID, hopefully Cellprofiler can separate these touching objects with the proper settings. Typically this is used to segment cells which are brightest at the center and dimmer near the edges of the cells however, it may work in this application. This module can declump adjacent objects based on the intensity of the objects. One idea is to use the IdentifyPrimaryObjects module on the Object Identities output image. 50x50 pixel) tiff sequence with touching objects I can test a few things since I haven’t used 3D data before. Maybe if you’re able to provide a cropped (e.g. Hi far as I’m aware there isn’t a direct way to use the Object Identities output in Cellprofiler for individual objects. Our goal being to segment complex structures like mitochondria and ER. Is there a better program for 3D segmentation that is more compatible with CellProfiler? We are looking for a program that can batch process the segmentation while incorporating more tools than what Cellprofiler currently provides.I tried this format with the 3D segmentation from Ilastik and was able to see the same greyscale coding of individual objects when viewed in ImageJ, but 1) I can’t get the file to open properly in CellProfiler, and 2) I think the metadata for z step interval is being lost during this export process. I have been able to do this with 2D images by exporting them as the uint16 format. Is there a compatible file format that I can use to export my segmented 3D image from Ilastik for use in CellProfiler without losing the segmentation between individual objects?.I can export the segmentation as a binary tiff sequence, but I lose the object segmentation information from Ilastik (i.e., separation between touching objects). My problem lies in exporting from Ilastik and importing into CellProfiler. I am now trying to use other programs, such as Ilastik, to do the 3D segmentations then import the segmentations into CellProfiler for quantification. The 3D segmentation tools in CellProfiler aren’t able to fully segment all of the organelles I am interested in (mitochondria, ER, golgi, peroxisomes, lipid droplets, lysosomes). I am trying to quantify organelle shape, size, and contacts (all from measurements within CellProfiler) from z-stack image series. ![]()
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