Data, code, and hardware specs associated with the Bryant et al manuscript, "The neural basis of heat seeking in a human-infective parasitic worm." Includes files related to the version in BioRxiv, as well as submissions to peer-reviewed journals, and final publication in Current Biology. The BioRxiv version can be accessed at this link.
Code freezes related to specific manuscript versions are saved as separate Releases, and archived using Zenodo.
Custom code for data acquisition and analysis. Folder includes the following subfolders:
- Calcium Imaging Preprocessing and Analysis: Used to align raw fluorescence values and temperature reads, plot traces, and quantify specific parameters related to calcium imaging.
- Plotting in R: Code written in R that generates various plots shown in the manuscript.
- Thermotaxis Worm Tracker v3: Matlab codebase for worm tracking using the thermotaxis area (version 3).
- Thermotaxis Worm Tracker v4: Matlab codebase for worm tracking using the thermotaxis area (version 4).
- Worm Tracking Camera Controls: Matlab functions for generating TTL pulse sequences via a Labjack USB DAQ device.
- Worm Tracking Preprocessing: FIJI/ImageJ Scripts for post hoc processing of worm tracking image sequences.
- Zeiss Zen Scripts: Scripts for aligning CFP/YFP signals following calcium imaging.
Includes parts lists and wiring diagrams for custom behavioral and imaging setups. Folder includes the following subfolders:
- Large Format Thermotaxis Arena: diagrams/parts lists/wiring diagrams related to the large format thermotaxis assay arena.
- Thermal Stimulator: parts lists for custom thermal stimulator, 3D printing a custom stage clamp, and Zeiss Zen scripts for preprocessing/aligning CFP/YFP raw acquisition data.
Includes data files containing raw data as well as processed/quantified data. Folder includes the following subfolders:
- Calcium Imaging: includes CVS files with CFP/YFP intensity values at soma and background regions of interest. Generated using Zeiss Zen scripts. Also includes .dat files with collated temperature recordings generated by ATEC302 software. Also includes Matlab .mat objects containing preprocessed and aligned YC3.60 imaging and temperature data.
- cGMP Imaging: includes Matlab .mat objects containing preprocessed and aligned FlincG3 imaging and temperature data.
- Worm Tracking: contains .xlsx files with raw data for worm tracking experiments (including: Ss-tax-4, Sr-gcy-23.2p::strHisCl1, reversal behaviors, and example positive thermotaxis). See internal readme file for more information.
Contains supplemental data files related to the BioRxiv version of the manuscript.
- Supplemental Data File 1: This file includes the results of statistical tests and exact p values, as well as the data used for statistical analyses in the BioRxiv version.
- Supplemental Data File 2: This file includes all primers, plasmids, worm strains, and thermal ramps used in the BioRxiv version.
Shield:
This work is licensed under a Creative Commons Attribution 4.0 International License.
