![]() ![]() DiameterJ is a validated nanofiber diameter characterization tool. You will find Labkit in the main menu under Plugins > Labkit. DiameterJ is a free, open source plugin created for ImageJ, ImageJ 2, and Fiji developed at the National Institute of Standards and Technology. ParticleinCell-3D is a freely available ImageJ macro. Methods: We developed a novel method to analyze stacks of confocal fluorescence images of single cells interacting with nano-and micro-particles. Finally, manual tools for ground-truth annotation are available. Aim: This study examines the absolute quantification of particle uptake into cells. Furthermore, memory efficient and fast random forest based pixel classification based on the Waikato Environment for Knowledge Analysis (WEKA) is implemented, optionally exploiting the power of graphics processing units (GPUs) to gain additional performance and can even be used on high performance computing clusters (HPC) for distributed processing of big image data. Especially the image processing package Fiji is a valuable and powerful extension of ImageJ. It is open-source software, platform-independent and enables students and researchers to obtain an easy but thorough introduction into image analysis. This efficiency is achieved by using Imglib2 and BigDataViewer as the foundation of our software. ImageJ is a versatile and powerful tool for quantitative image analysis in microscopy. Labkit is specifically designed to work efficiently on big image data and users of consumer laptops can conveniently work with multiple terabytes large image data. The plugin can be found in the Analyze > Colocalization menu after it has been installed. To address these limitations, we established a unifying framework for neuronal morphometry and analysis of single-cell connectomics for the widely used Fiji and ImageJ platforms 2,3. It offers easy to use manual and automated image segmentation routines that can be rapidly applied to single- and multi-channel images as well as timelapse movies in 2D or 3D. Additionally, the images (particularly 3D) need to be correctly scaled (Image > Properties), otherwise all axes will be assumed to have the same scale and your mean correlation distance will be in pixels. We would really appreciate tips from more experienced users on how to improve our results.Labkit is a user-friendly Fiji plugin for the segmentation of microscopy image data. It’s our first time trying to segment cells. Our best results are with automatic seeds and a radius of 25 px (that’s approx the size of a cell). For example, using the probability map from Weka Segmentation as seeds doesn’t seem to help. We have also tried playing around with the parameters for the watershed split. See the main repository for links to our publications and the full-featured Python package that can also be used to train new models. We tried retraining the algorithm in the Weka segmentation several times, but don’t know how to further improve the outcome. This is the ImageJ/Fiji plugin for StarDist, a cell/nuclei detection method for microscopy images with star-convex shape priors.The plugin can be used to apply already trained models to new images. The issue is that we must keep the shape of our blobs with several cells stuck together for the watershed to be able to split them. I’m not sure Gaussian Blur is helping much since we must use very low sigma values (about 1). Erosion is definitely not helpful in our case. Convert results to 8-bit grayscale, fill holes and apply Gaussian blur 3D.Īfter segmenting, we tried several filters.It can be used as a standalone program or from withing SNT. After watching many videos (there’s great material online!) and reading posts in this forum, we’ve set the following pipeline: SNT’s Reconstruction Viewer is a powerful OpenGL 3D visualization tool for both surface meshes and reconstructions. We’re convinced they can be improved, but don’t know how to go about it. We’re trying to segment and count EdU-stained cell nuclei in a stack of images and we’re not quite happy with the results to date. ![]()
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