Axonal fiber quantification in fluorescence images

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A set of Fiji macros for axonal fiber quantification in fluorescence images. These macros were developed for the study: Fasting Induces Remodeling Of The Orexigenic Projections From The Arcuate Nucleus To The Hypothalamic Paraventricular Nucleus, In A Growth Hormone Secretagogue Receptor-Dependent Manner Cabral A, Fernandez G, Tolosa MJ, Rey-Moggia Á, Calfa G, De Francesco PN, Perello M. Molecular Metabolism, 2019, https://doi.org/10.1016/j.molmet.2019.11.014. Description This package contains a set of Fiji macros developed to quantify axonal fibers within the mouse brain in fluorescence miscroscopy images. Contents fiber_quantification_IF_FP.ijm macro to quantify fluo-immunolabeled/fluorescent protein expressing fibers at high magnification. fiber_quantification_DiI.ijm macro to quantifiy fibers labelel with DiI tracer at medium magnification. A folder to install the auxiliary thresholding function Gaussian_threshold_function.ijm. It is part of the InstantFunctions collection (https://github.com/ndefrancesco/InstantFunctions). A folder with a macro for pre-processing DiI-stacks. A folder with test images and rois. Prerequisites: Fiji (https://fiji.sc) installed Installation/use: Download the package and decompress to some location in your computer. Copy the contents of the "install_function" folder into the "macros" folder inside Fiji. Start Fiji. The thresholding function will be now available. Open an image to process Run the apropiate macro file (via Plugins > Macros > Run..., or by opening and running from the script editor) A table of results will be generated. Following runs will continue populating this table. These macros can be called inside a batch macro to process a collection of images, or from a macro set to facilitate its manual use.

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