Axonal fiber quantification in fluorescence images

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:

1. Download the package and decompress to some location in your computer.
2. Copy the contents of the "install_function" folder into the "macros" folder inside Fiji.
3. Start Fiji. The thresholding function will be now available.
4. Open an image to process
5. Run the apropiate macro file (via Plugins > Macros > Run..., or by opening and running from the script editor)
6. 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.