Henley, M. | bioRxiv Science

bioRxiv2024

AutoMorFi: Automated Whole-image Morphometry in Fiji/ImageJ for Diverse Image Analysis Needs

Running on the highly popular and accessible ImageJ/Fiji platform for biological image analysis, we have established AutoMorFi as a streamlined interface for automated whole-image morphometric analysis that generates at least 47 measurements per cell or object in under 1 minute. We performed multiple validated cluster and principal component analyses on nonredundant morphometric parameters derived from AutoMorFi for various cell types, objects, and organisms. We used images of rodent macrophages, human postmortem brain tissues from multiple sclerosis (MS) and Alzheimers disease (AD) patients, iPSC/animal models for Downs syndrome and autism spectrum disorder (ASD), and organisms such as sea anemone and corals. AutoMorFis adaptability extends across diverse imaging modalities including brightfield, confocal, or widefield fluorescence microscopy as well as underwater photography. Due to its unlimited and unbiased sampling across any image and high potential for modification and customization, using AutoMorFi has led to the discovery of new distinguishing features in previously studied cell types and organisms as well as the development of rapid diagnostic approaches. AutoMorFi represents a transformative tool that will accelerate morphometric analysis and offer broad relevance in biological studies.

cell biology↗

bioRxiv2019

Do African savanna elephants (Loxodonta africana) eat crops because they crave micronutrients?

O_LIElephants can cause negative consequences for both themselves and for humans by consuming agricultural crops. It is unclear whether savanna elephant crop consumption is merely opportunistic behaviour or related to insufficient quality of natural forage. We analysed the role of vegetation quality on elephant crop consumption. We focused on the role of micronutrients, as natural elephant diets are thought to be insufficient in elements such as sodium and phosporus, which can influence their foraging decisions.\nC_LIO_LIFor 12 months across four seasons we collected elephant feeding trail data along with tree, grass and crop samples. We investigated how the quality and availability of these items influenced elephant dietary choices across months and seasons. Subsequently, we compared levels of fibre, digestible energy, dry matter intake, and micronutrients, together with secondary compounds (tannins) across the three vegetation groups. As elephants do not make dietary choices based on one component, we also analysed the nutrient balance of food items with right-angle mixture models.\nC_LIO_LIThe levels of phosphorus, magnesium and dry matter intake corresponded to foraging preference. Compared to trees and grasses, crops contained significantly higher amounts of digestible energy content, dry matter intake, nitrogen, phosphorus, calcium and magnesium. PCA results showed that crops differed in phosphorus and magnesium levels. The right-angle mixture models indicated that except for one tree species, all food items elephants consumed were relatively deficient in phosphorus.\nC_LIO_LIThe combined results of these analyses suggest a phosphorus deficiency in elephant diet in northern Botswana. Crops, with their high absolute phosphorus levels and dry matter intake, provide an alternative source of phosphorus to reduce the deficiency. This may explain the high intensity of crop consumption in the wet season in our study area. A potential mitigation measure against elephant crop consumption might be to provide supplementary phosphorus sources.\nC_LI

ecology↗