Avoid discipline-specific terminology ("jargon").
Screenshots (to help identify issues with tools or features).Annotated Mock-ups (showing what features you are trying to measure).Reference Images (taken from published papers).Example Images (what you want to analyze).Images give everyone a chance to understand the problem.Notes on Quality Questions & Productive Participation I'm fairly new to ImageJ and don't know the best methods.Īny help and advice would be appreciated. I'm hoping someone here with more experience might be able to help me. So long as my sample preparation and image capture is consistent (which is it's own issue entirely) this shouldn't be a hard problem. Then I can count the particles with ease. Big thanks to them for creating thisīasically what I am trying to do is turn this image into this image(but better) using image segmentation. This issue has been solved using Stack Contrast Adjustment Plugin. What would be the best way to automatically adjust BC for a group of images to some level that I set, like a reference image? Normalize histogram and brightness usually goes way to far and isn't helpful. The BC on each image sometimes differs and it is up to me to manually adjust it so they all look the same and I can run a batch analysis on them. I'm just measuring the black interiors.Īnother, much simpler, issue is image consistency. This helps but some of the smaller less defined particles are still difficult to see. To get rid of the white halo around the particles (or pits rather) I perform a grey morphology filter and adjust the BC. There are so many options in Weka I'm not even sure which would best suit my analysis. Currently I am using Weka Trainable Image Segmentation (in Fiji) for this and it's given me the best results but it still struggles. I need to segment them so that I can count the particles and analyze their shape, distribution, aspect ratio, etc automatically. This is what my images tend to look like. One of the biggest issues I'm encountering is consistent particle counting for my images. I'm currently working through a project that involves a fair bit of image capture, processing, and analysis. 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."
IMAGEJ PARTICLE ANALYSIS FULL
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.
IMAGEJ PARTICLE ANALYSIS SOFTWARE
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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