Software Research Tools

We make all of this code publicly available here to satisfy a large number of requests, along with instructions to help you get started. We encourage groups and researchers who have an interest in using these algorithms to do so freely, and request only that it be referenced properly. Many groups contact us with specific questions or comments, and we enjoy being able to contribute while hearing about new and interesting science!

Most of the code found here is written in MATLAB.
New! We have written the 2D and 3D centroid feature finding and tracking code in Python, a free, open source platform. This code has been completely tested and found to have identical accuracy to the corresponding MATLAB code; and faster runtime.

MATLAB 3D feature finding algorithms
download all (.zip)
bpass3dMB.m
feature3dMB.m
FFindinstruct.txt
fracshift3dMB.m
llmx3dMB.m
lrsqd3dMB.m
make_arr.m
The key publication relating to the development of these 3D particle identification and tracking programs is here.

MATLAB particle pretracking and tracking, and 2D feature finding
download all (.zip)
The publication for which the tracking algorithm was developed and first used, and in which the localization resolution of the feature finding in 2D are reported, is here.

Individual files
Instruct_feature_track_pretrack.pdf
bpass.m
fancytrack.m
feat_find_init.m
feature2D.m
feature2D_nodilate.m
fieldof.m
fracshift.m
localmax.m
localmax_nodilate.m
luberize.m
mpretrack_init.m
mpretrack.m
rsqd.m
thetarr.m
trackmem.m
unq.m


Microrheology
download all (.zip)
A publication reporting data obtained using these microrheology algorithms is here.

Instructions_microrheology.pdf
Dedrifting and conversions
conversions_no_dd.m
dedrifting_and_conversions.m
dedrift.m
drift_loop.m
from_8_columnns_to_4.m
gdxtrinterp.m
getdx.m
getting_individual_beads.m
mot_eintegrate.m
motion.m
pixtomicro.m
putting_in_missing_frames.m
smooth_d.m
Moduli
calc_G.m
logderive.m
polyfitw.m
MSD
calc_rg_k.m
making_logarithmically_space_msd_vs_tau.m
Mean_SD_many_single_beads_E.m
Mean_SD_many_single_beads.m
Rg_matrix_many_single_beads.m
Two_point
calling_two_fitting_methods.m
errorbarlogx.m
fitting_to_line_shell.m
fitting_r_times_Drr_Dqq_shell.m
get_corr.m
laccumulate.m
lfit.m
ltrinterp.m
msddE.m
msdd.m
number_of_points_per_r.m
plot_poisson.m
poisson_from_msdd.m
separating_beads_by_FOV.m
twopoint.m

Particle pretracking & tracking and 2D feature finding in Python
download all (.zip)
Instruct_Py_feat_track_pretrack.pdf
bpass.py
create_mask.py
fancytrack.py
feature2D.py
fieldof.py
fracshift.py
localmax.py
luberize.py
mpretrack.py
tiff_file.py
trackmem.py
unq.py

Python 3D feature finding algorithms
It's time to put away your software maintenance subscriptions, fire up your open source Python platform, put these kids together (in the same directory), and enjoy the sweet taste of freedom.
download all (.zip)
bpass3dMB.py
feature3D.py
FFindinstruct.txt
fracshift3D.py
isinstack.py
llmx3D.py
lrsqd3D.py
make_arr.py
nlparci.py
The key publication relating to the development of these 3D particle identification and tracking programs is here.