Data from: Scoring thermal limits in small insects using open-source, computer assisted motion detection
Data files
Sep 05, 2023 version files 9.30 GB
-
Additional_insects.zip
-
Computer_estimates.zip
-
DIME.zip
-
Human_interobserver.zip
-
README.md
-
Videos.zip
Abstract
Scoring large amounts of thermal tolerance traits live or with recorded video can be time consuming and susceptible to investigator bias, and as with many physiological measurements, there can be trade-offs between accuracy and throughput. Recent studies show that particle tracking is a viable alternative to manually scoring videos, although it may not detect subtle movements, and many of the software options are proprietary and costly. In this study, we present a novel strategy for automated scoring of thermal tolerance videos by inferring motor activity with motion detection using an open-source Python command line application called DIME (Detector of Insect Motion Endpoint). We apply our strategy to both dynamic and static thermal tolerance assays, and our results indicate that DIME can accurately measure thermal acclimation responses, generally agrees with visual estimates of thermal limits, and can significantly increase the throughput over manual methods.
README: Pixel change dataset
Abbreviations
CTMAX = Critical thermal maximaCTMAX
CTMIN = Critical thermal minima
CCRT = Chill coma recovery time
HKDT = Heat knock down time
IM = Individual Median
OT = Optimal Threshold
CP = Change Point
This dataset contains the raw data used to validate automatic scoring methodologies for thermal limit bioassays in small insects. Apart from the main insect thermal performance data, we include an inter-observer dataset comparing three human estimates. Finally, a last dataset containing computer and human CTmax estimates of six additonal species is also provided. The original videos used for each scoring are also included. Four bioassays were evaluated: Critical thermal maxima (CTMAX), Critical thermal minima (CTMIN), Chill coma recovey time (CCRT), and Heat knock down time (HKDT).
Description of the data and file structure
Directory: /Computer_estimates
Computer and visual estimates of each bioassay in files ending in "_dataset.csv".
Columns: "well_name", "well", "visual_estimate", "changepoint_estimate", "individualmedian_estimate", "optimalthreshold_estimate" (aka MacLean2022), and "block".
The analysis parameters used for DIME, the number of individuals removed and the total number of observations are collected in the file "Video_parameter_key.xlsx".
The files ending in "temp_dataset" are expressed in temperature units (degrees Celsius), while those only with "_dataset" are in minutes.Line parameters extracted from temperature data per block are included in file ending with "_lineParameters.csv" for CTmin and CTmax datasets. Columns are "block", "slope", "intercept", "r-squared". The units for slope are "degree Celsius / minute" and intercept are "degree Celsius".
TreatmentTable.csv file contains the experimental design. Columns: "Well", "treatment", "sex" and "temp". These are the same for every 30-well block in this directory. In the sex column, m = male and f = female. In the temp column, the treatments are three possible (18, 25, 30) and their units are degree Celsius.
Treatment key
A = 18C + male,
B = 18C + female,
C = 30 C + male,
D = 30C + female,
E = 25C + male,
F = 25C + female
Directory: /Human_interobserver
Four files ending in "_interobserver.csv" contain visual estimates by three human observers. The units of every file are in "minutes". Just one out of three blocks per bioassay was analyzed (see source data key below). Missing data correspond to removed or missing individuals, namely in HKDT individual 16 and CCRT individual 2. Columns: "well", "Observer1", "Observer2", "Observer3".
Source data key
CTMAX: block 1
CTMIN: block 2
HKDT: block 1
CCRT: block 2
Directory: /Additional_insects
CTmax estimates of 6 additional species are included in file "Ctmax-insects.csv". There are three columns included, "species", "visual" and "IM". The last two columns indicate the CTmax by visual estimation and with the algorithm Individual Mean, respectively. The unit for both variables is "degrees Celsius"
Directory: /Videos
Video files per bioassay are included, three videos per bioassay.
Code
The code used for this analysis can be found in https://github.com/fernan9/DIME
A copy of the main code "dime_1_1.py", its README file and two R scripts for further analysis are included in the directory "DIME"
Methods
Data is collected from observing videos from bioassays which are scored by humans or by an algorithm using the proposed tool DIME.
Usage notes
DIME open source can be found at https://github.com/fernan9/DIME