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Simple Summary  Studying insect physiology frequently involves assessment of certain characteristics including body size and temperature tolerance. Information on organismal traits such as body size and temperature tolerance is typically obtained by weighing or measuring individuals or by visual observation of time points or temperatures where insects lose the ability to move when exposed to stressful temperatures. Such manual methods can be time consuming, tedious and prone to human error. Therefore, accurate automated methods, with the potential to increase the number of analysed individuals, are needed. In this study, we used image analysis software to measure thermal tolerances and larval body sizes in houseflies and black soldier flies and compared the results with those obtained manually. We found a strong correlation between larval body sizes measured using the two methods and were able to decrease the time spent on the measurements markedly. We did not find the same values for temperature tolerance using the two methods, but we often found the same relationship between groups that we compared. In addition, the automated method allowed us to track the movements of the flies over long periods of time, thus increasing the information output from the experiments. We conclude that implementation of automated methods will bring new opportunities within insect research.    Abstract  Within ecophysiological and genetic studies on insects, morphological and physiological traits are commonly assessed and phenotypes are typically obtained from manual measurements on numerous individuals. Manual observations are, however, time consuming, can introduce observer bias and are prone to human error. Here, we contrast results obtained from manual assessment of larval size and thermal tolerance traits in black soldier flies ( Hermetia illucens ) and houseflies ( Musca domestica ) that have been acclimated under three different temperature regimes with those obtained automatically using an image analysis software (Noldus EthoVision XT). We found that (i) larval size estimates of both species, obtained by manual weighing or by using the software, were highly correlated, (ii) measures of heat and cold tolerance using manual and automated approaches provided qualitatively similar results, and (iii) by using the software we obtained quantifiable information on stress responses and acclimation effects of potentially higher ecological relevance than the endpoint traits that are typically assessed when manual assessments are used. Based on these findings, we argue that automated assessment of insect stress responses and largescale phenotyping of morphological traits such as size will provide new opportunities within many disciplines where accurate and largescale phenotyping of insects is required.

Contrasting Manual and Automated Assessment of Thermal Stress Responses and Larval Body Size in Black Soldier Flies and Houseflies