Script for stitching of image data obtained by multimode fibre based holographic endoscope
Authors/Creators
Description
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
