Threshold and select objects imagej4/12/2024 ![]() Note that the plugin expects bright objects on dark background, so you might want to call Edit › Invert if your input image has dark objects. Load an single channel image (8-bit, 16-bit or 32-bit). There is little performance loss by decreasing the size of the smallest leaflet. However, a good guide is to match the size of the smallest leaflet to something just larger than the size of the smallest object expected. As with the noise estimate and scaling factor, determining the appropriate minimum quadtree leaflet size is best done with experiment. The user also controls the size of the smallest quadtree region (aka leaflet). Once the regional thresholds are computed, they are interpolated (bilinear interpolation) across the entire image yielding a threshold map. In our experience, regional threshold failures are rare. It is possible that thresholds fail all the way up the quadtree heirarchy, in which case a same threshold is applied to all regions which is identical to applying a global threshold. In such cases, the regional threshold is replaced by the threshold of its parent quadtree (if the parent's threshold doesn't fail). Occasionally, the regional threshold fails if the sum of the weights (the denominator) falls to the level of background containing only noise. Btw, I don't have access to photoshop where recolouring and combining these images would be easy.Error creating thumbnail: Unable to save thumbnail to destination I tried weka segmentation but the results were not good enough. Knowledge with Fiji: I can use threshold to select one colour. and how do I overlay this? Some of the areas selected in the second image (dark beiges) also include areas from the first image (blues), thus this image would need to be at the bottom and the first one at the top.a bit of smoothing of sorts might be useful to eliminate or add single pixels.flood fill tool doens't seem to colour in disconnected areas, and most are disconnected and very tiny. the second image is b/w but I need it to be red/white.I want these areas to appear red in the final image. use green channel and select darker beige areas seems to work best. ![]() use red channel to select blue area with threshold.In the end I want to have an image consisting of a white background, and red and black areas. I'm trying to select blue and darker beige colours from an image containing blues, brigher and darker beiges. ¹This subreddit is not affiliated with the creators of ImageJ or FIJI, but is simply a place to share ideas, papers, resources, and expertise - especially as relate to questions & answers posted here. Sign-up for one of the mailing lists: /Mailing_Lists It also hosts a forum for interacting with the developers.įIJI Is Just ImageJ - "a distribution of ImageJ (and ImageJ2) together with Java, Java3D and a lot of plugins organized into a coherent menu structure." is full of ImageJ development and analysis resources. Image analysis is interdisciplinary, so clearly explain field-specific terms or jargon. Clearly explain what you are trying to learn, not just the method used, to avoid the XY problem. Provide details: Be thorough in outlining the question(s) that you are trying to answer.People from the future may be stuck trying to answer the same question. Report spam or content that is hateful or off-topic.Upvote those who contribute to the discussion and provide freely of their time to assist you.Projects: Share a Link to your pet image analysis project.Research: Links to published (articles in scientific journals or in established repositories) that utilize ImageJ/FIJI for image analysis or are about image analysis.Discussions: Text posts, meant to ask about general issues relating to image analysis.Image analyst job posts are also welcome. Tips: Text or Link posts to share useful how-to tricks and discoveries on using ImageJ/FIJI.Questions which have been Solved will be marked as such. This could include algorithms, microscopy and scientific imaging, plug-ins, methods, and specific features of the software. Questions: Text posts asking about image analysis and ImageJ/FIJI.This is a an unofficial¹ forum to discuss image analysis, software features, to get help, to share ideas, and to share work done using ImageJ or FIJI. It's used worldwide, by a broad range of scientists. ImageJ is a freely available, open source image processing and analysis program using Java, on which FIJI is based.
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