Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji 24 leverages the updated ImageJ2 framework, which contains elements from ImageJ1 via the optional ImageJ Legacy bridge that facilitates full backwards compatibility. Importantly, the process still allows the operator to evaluate and have control over all the phases of quantification process.ĬMA: chaperone-mediated autophagy CSV: comma separated values eMI: endosomal microautophagy Fiji: Fiji is just ImageJ MA: macroautophagy SParQ: Streamlined Particle Quantification.įiji ImageJ autophagy endosomes lysosomes proteostasis. Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. To streamline the process, we developed a plug-in that, integrated into Fiji, enables the automated quantification of vesicular (i.e. ImageJ.exe supports file-associations, drag and drop, auto-configuration and command line operation. All versions include ImageJ.exe, a Windows program contributed by George Silva that launches ImageJ (ij.jar). Typically, the images are analyzed individually with software such as the widely available Fiji/ImageJ (), adjusting and thresholding each image and channel independently, which is a very labor intensive and fastidious task. The Windows version of ImageJ is available bundled with either Java 6 or Java 8, and without Java. Detailed analyses require quantification of hundreds of structures under various conditions. via autophagy) is by labeling vesicular structures such as endosomes, autophagosomes, lysosomes, or model substrates with fluorescent tags or by fluorescent antibody staining. Fiji is an image processing packagea batteries-included distribution of ImageJ2, bundling a lot of plugins which facilitate scientific image analysis. A common way of studying protein transport and degradation (e.g. ImageJ 1 is a powerful, oft-referenced platform for image processing, developed by Wayne Rasband at the National Institutes of Health (NIH). The clock scan protocol for image analysis is an efficient tool to quantify the average pixel intensity within, at the border, and outside (background) a closed or segmented convex-shaped region of interest, leading to the generation of an averaged integral radial pixel-intensity profile. The endolysosomal system is critical for protein homeostasis in cells.
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