RLNEK 1.0.7

RLNEK is a package to analyze data taken from Trackmate on receptor-ligand kinetics. GitHub: https://github.com/zrollins/RLNEK

Corresponding Manuscript: "Receptor-Ligand Non-Equilibrium Kinetics (RLNEK) 1.0: An Integrated Trackmate Laminar Flow Chamber Analysis"

Trackmate Dependencies:

=ImageJ 2.3.0/1.53f51 =Java 1.8.0_301 [64-bit] =Trackmate v7.4.0

RLNEK Dependencies:

= Python 3.7 = pandas 1.3.5 = numpy 1.22.0 = scipy 1.7.3 = matplotlib 3.5.1

RLNEK Modules: Module 0A - convert flow rate to applied tether/tensile force Module 0B - determine non-specific bond lifetime Module 0C - determine if coating concentration/site density range meets single-molecule criteria Module 1 - determine Nb/NT & koff @ various flow rates, coating concentrations NT Optimization - optimize NT values for given flow rate across various site densities (precursor to Module 2) Module 2 - determine Nb/NT, koff, k+, & kin @ various flow rates, site densities

Tips:

1. Please read manuscript and corresponding User Guide to understand experimental parameters and data necessary to perform calculations.
2. In previous versions of Trackmate, the files are outputted in different formats. Ensure that Trackmate "tracks" and "spots" files are formatted correctly (e.g., in the "spots" file, particleIDS are listed in numerical order of trackIDs & numerical order of frames). Use provided test files as a reference.
3. All modules can handle replicates for a given condition. Please see test folders for implementation.
4. Collect Receptor-Ligand Non-Equilibrium Kinetics.

Appendix: Nb = number of cells/spheres bound NT = total number of cells/spheres to cross field of view Nb/NT = capture efficiency koff = force-dependent dissociation rate (1/ bond lifetime) k+ = effective on rate of cell/spheres (includes diffusive & kinetic timescales) kin = intrinsic on rate of receptor-ligand pair (assumed constant) Extension of variable names/descriptions: "appendix.pdf"

Test files: Data files to test the functionality of RLNEK are provided in the "RLNEK_tests" folder. Module_0A_test contains files to be used to test Module_0A, Module_0B_test contains files to be used to test Module_0B, etc.

Digitized Data: Data that was digitized from previous manuscripts and used in this RLNEK manuscript is provided in the "Digitized_Data" folder.

Copyright Notice: Copyright 2021-2022 Allison Chan, Zachary A Rollins, Venktesh S. Shirure, Steven C. George, and The Regents of the University of California

License Notice: This file is part of RLNEK.

RLNEK is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

RLNEK is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with RLNEK. If not, see https://www.gnu.org/licenses/.