Stitching of 3D image stack obtained by constant speed insertion of multimode optical fibre endoscope PACKAGE CONTENTS stitch3d_win9planes.m a script that accesses data from 3D stack of images obtained by a constant speed insertion at different sample depth findspeed.m a helper function that evaluates the speed of probe insertion in the 3D images stack SYSTEM REQUIREMENTS OS: any (tested on Ubuntu Linux, MacOS) MathWorks MATLAB installed (tested on R2017a, R2021a) INSTALLATION INSTRUCTIONS none, in MATLAB command line enter folder containing scripts and data file(s) RUNNING ANALYSIS run stitch3d_win9planes from MATLAB command line EXPECTED OUTPUTS MATLAB figure with an animation showing the stitched image for various imaging focal planes MATLAB variables "colimdats" and "colimdatsU8" containing the stitched images (3D stacks) in double or uint8 format data correspond to "fluorescent black-green" colormap file "depth_demo.gif" that contains the animated image expected runtime less than 10 seconds INSTRUCTIONS FOR USE in script "stitch3d_win9planes.m" change variable "fname" in order to use different data set. in script "democode_blood_flow_speed_tracker.m" change variable "outputname" in order to change the name of the output animation gif-file