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Abstract Phenological shifts across plant species is a powerful indicator to quantify the effects of climate change. Today, mobile applications with automated species identification open new possibilities for phenological monitoring across space and time. Here, we introduce an innovative spatio‐temporal machine learning methodology that harnesses such crowd‐sourced data to quantify phenological dynamics across taxa, space and time. Our algorithm links individual phenological responses across thousands of species and geographical locations, using a similarity measure. The analysis draws on nearly ten million plant observations collected through the AI‐based plant identification app Flora Incognita in Germany from 2018 to 2021. Our method quantifies changes in synchronisation across the annual cycle. During the growing season, synchronised behaviour can be encoded by a few characteristic macrophenological patterns. Nonlinear spatio‐temporal changes of these patterns can be efficiently quantified using a data compressibility measure. Outside the growing season, the phenological synchronisation diminishes introducing noise into the patterns. Despite biases and uncertainties associated with crowd‐sourced data, for example due to human data collection behaviour, our study demonstrates the feasibility of deriving meaningful indicators for monitoring plant macrophenology from individual plant observations. As crowd‐sourced databases continue to expand, our approach holds promise to study climate‐induced phenological shifts and feedback loops.

Abstract Opportunistic plant records provide a rapidly growing source of spatiotemporal plant observation data. Here, we used such data to explore the question whether they can be used to detect changes in species phenologies. Examining 19 herbaceous and one woody plant species in two consecutive years across Europe, we observed significant shifts in their flowering phenology, being more pronounced for spring-flowering species (6-17 days) compared to summer-flowering species (1-6 days). Moreover, we show that these data are suitable to model large-scale relationships such as “Hopkins’ bioclimatic law” which quantifies the phenological delay with increasing elevation, latitude, and longitude. Here, we observe spatial shifts, ranging from –5 to 50 days per 1000 m elevation to latitudinal shifts ranging from –1 to 4 days per degree northwards, and longitudinal shifts ranging from –1 to 1 day per degree eastwards, depending on the species. Our findings show that the increasing volume of purely opportunistic plant observation data already provides reliable phenological information, and therewith can be used to support global, high-resolution phenology monitoring in the face of ongoing climate change.

Abstract We present a multidisciplinary forest ecosystem 3D perception dataset. The dataset was collected in the Hainich-Dün region in central Germany, which includes two dedicated areas, which are part of the Biodiversity Exploratories - a long term research platform for comparative and experimental biodiversity and ecosystem research. The dataset combines several disciplines, including computer science and robotics, biology, bio-geochemistry, and forestry science. We present results for common 3D perception tasks, including classification, depth estimation, localization, and path planning. We combine the full suite of modern perception sensors, including high-resolution fisheye cameras, 3D dense LiDAR, differential GPS, and an inertial measurement unit, with ecological metadata of the area, including stand age, diameter, exact 3D position, and species. The dataset consists of three hand held measurement series taken from sensors mounted on a UAV during each of three seasons: winter, spring, and early summer. This enables new research opportunities and paves the way for testing forest environment 3D perception tasks and mission set automation for robotics.

Plant phenology plays a vital role in assessing climate change. To monitor this, individual plants are traditionally visited and observed by trained volunteers organized in national or international networks - in Germany, for example, by the German Weather Service, DWD. However, their number of observers is continuously decreasing. In this study, we explore the feasibility of using opportunistically captured plant observations, collected via the plant identification app Flora Incognita to determine the onset of flowering and, based on that, create interpolation maps comparable to those of the DWD. Therefore, the opportunistic observations of 17 species collected in 2020 and 2021 were assigned to “Flora Incognita stations” based on location and altitude in order to mimic the network of stations forming the data basis for the interpolation conducted by the DWD. From the distribution of observations, the percentile representing onset of flowering date was calculated using a parametric bootstrapping approach and then interpolated following the same process as applied by the DWD. Our results show that for frequently observed, herbaceous and conspicuous species, the patterns of onset of flowering were similar and comparable between both data sources. We argue that a prominent flowering stage is crucial for accurately determining the onset of flowering from opportunistic plant observations, and we discuss additional factors, such as species distribution, location bias and societal events contributing to the differences among species and phenology data. In conclusion, our study demonstrates that the phenological monitoring of certain species can benefit from incorporating opportunistic plant observations. Furthermore, we highlight the potential to expand the taxonomic range of monitored species for phenological stage assessment through opportunistic plant observation data.

Abstract Accurate species identification is essential for ecological monitoring and biodiversity conservation. Interactive plant identification keys have been considerably improved in recent years, mainly by providing iconic symbols, illustrations, or images for the users, as these keys are also commonly used by people with relatively little plant knowledge. Only a few studies have investigated how well morphological characteristics can be recognized and correctly identified by people, which is ultimately the basis of an identification key's success. This study consists of a systematic evaluation of people's abilities in identifying plant‐specific morphological characters. We conducted an online survey where 484 participants were asked to identify 25 different plant character states on six images showing a plant from different perspectives. We found that survey participants correctly identified 79% of the plant characters, with botanical novices with little or no previous experience in plant identification performing slightly worse than experienced botanists. We also found that flower characters are more often correctly identified than leaf characteristics and that characters with more states resulted in higher identification errors. Additionally, the longer the time a participant needed for answering, the higher the probability of a wrong answer. Understanding what influences users' plant character identification abilities can improve the development of interactive identification keys, for example, by designing keys that adapt to novices as well as experts. Furthermore, our study can act as a blueprint for the empirical evaluation of identifications keys. Read the free Plain Language Summary for this article on the Journal blog.

Plant species complexes represent a particularly interesting example of taxonomically complex groups (TCGs), linking hybridization, apomixis, and polyploidy with complex morphological patterns. In such TCGs, mosaic-like character combinations and conflicts of morphological data with molecular phylogenies present a major problem for species classification. Here, we used the large polyploid apomictic European Ranunculus auricomus complex to study relationships among five diploid sexual progenitor species and 75 polyploid apomictic derivate taxa, based on geometric morphometrics using 11,690 landmarked objects (basal and stem leaves, receptacles), genomic data (97,312 RAD-Seq loci, 48 phased target enrichment genes, 71 plastid regions) from 220 populations. We showed that (1) observed genomic clusters correspond to morphological groupings based on basal leaves and concatenated traits, and morphological groups were best resolved with RAD-Seq data; (2) described apomictic taxa usually overlap within trait morphospace except for those taxa at the space edges; (3) apomictic phenotypes are highly influenced by parental subgenome composition and to a lesser extent by climatic factors; and (4) allopolyploid apomictic taxa, compared to their sexual progenitor, resemble a mosaic of ecological and morphological intermediate to transgressive biotypes. The joint evaluation of phylogenomic, phenotypic, reproductive, and ecological data supports a revision of purely descriptive, subjective traditional morphological classifications.

Abstract Background Digital plant images are becoming increasingly important. First, given a large number of images deep learning algorithms can be trained to automatically identify plants. Second, structured image-based observations provide information about plant morphological characteristics. Finally in the course of digitalization, digital plant collections receive more and more interest in schools and universities. Results We developed a freely available mobile application called Flora Capture allowing users to collect series of plant images from predefined perspectives. These images, together with accompanying metadata, are transferred to a central project server where each observation is reviewed and validated by a team of botanical experts. Currently, more than 4800 plant species, naturally occurring in the Central European region, are covered by the application. More than 200,000 images, depicting more than 1700 plant species, have been collected by thousands of users since the initial app release in 2016. Conclusion Flora Capture allows experts, laymen and citizen scientists to collect a digital herbarium and share structured multi-modal observations of plants. Collected images contribute, e.g., to the training of plant identification algorithms, but also suit educational purposes. Additionally, presence records collected with each observation allow contribute to verifiable records of plant occurrences across the world.

Climate change represents one of the most critical threats to biodiversity with far-reaching consequences for species interactions, the functioning of ecosystems, or the assembly of biotic communities. Plant phenology research has gained increasing attention as the timing of periodic events in plants is strongly affected by seasonal and interannual climate variation. Recent technological development allowed us to gather invaluable data at a variety of spatial and ecological scales. The feasibility of phenological monitoring today and in the future depends heavily on developing tools capable of efficiently analyzing these enormous amounts of data. Deep Neural Networks learn representations from data with impressive accuracy and lead to significant breakthroughs in, e.g., image processing. This article is the first systematic literature review aiming to thoroughly analyze all primary studies on deep learning approaches in plant phenology research. In a multi-stage process, we selected 24 peer-reviewed studies published in the last five years (2016–2021). After carefully analyzing these studies, we describe the applied methods categorized according to the studied phenological stages, vegetation type, spatial scale, data acquisition- and deep learning methods. Furthermore, we identify and discuss research trends and highlight promising future directions. We present a systematic overview of previously applied methods on different tasks that can guide this emerging complex research field.

Poaceae represent one of the largest plant families in the world. Many species are of great economic importance as food and forage plants while others represent important weeds in agriculture. Although a large number of studies currently address the question of how plants can be best recognized on images, there is a lack of studies evaluating specific approaches for uniform species groups considered difficult to identify because they lack obvious visual characteristics. Poaceae represent an example of such a species group, especially when they are non-flowering. Here we present the results from an experiment to automatically identify Poaceae species based on images depicting six well-defined perspectives. One perspective shows the inflorescence while the others show vegetative parts of the plant such as the collar region with the ligule, adaxial and abaxial side of the leaf and culm nodes. For each species we collected 80 observations, each representing a series of six images taken with a smartphone camera. We extract feature representations from the images using five different convolutional neural networks (CNN) trained on objects from different domains and classify them using four state-of-the art classification algorithms. We combine these perspectives via score level fusion. In order to evaluate the potential of identifying non-flowering Poaceae we separately compared perspective combinations either comprising inflorescences or not. We find that for a fusion of all six perspectives, using the best combination of feature extraction CNN and classifier, an accuracy of 96.1% can be achieved. Without the inflorescence, the overall accuracy is still as high as 90.3%. In all but one case the perspective conveying the most information about the species (excluding inflorescence) is the ligule in frontal view. Our results show that even species considered very difficult to identify can achieve high accuracies in automatic identification as long as images depicting suitable perspectives are available. We suggest that our approach could be transferred to other difficult-to-distinguish species groups in order to identify the most relevant perspectives.

Abstract Background Deep learning algorithms for automated plant identification need large quantities of precisely labelled images in order to produce reliable classification results. Here, we explore what kind of perspectives and their combinations contain more characteristic information and therefore allow for higher identification accuracy. Results We developed an image-capturing scheme to create observations of flowering plants. Each observation comprises five in-situ images of the same individual from predefined perspectives (entire plant, flower frontal- and lateral view, leaf top- and back side view). We collected a completely balanced dataset comprising 100 observations for each of 101 species with an emphasis on groups of conspecific and visually similar species including twelve Poaceae species. We used this dataset to train convolutional neural networks and determine the prediction accuracy for each single perspective and their combinations via score level fusion. Top-1 accuracies ranged between 77% (entire plant) and 97% (fusion of all perspectives) when averaged across species. Flower frontal view achieved the highest accuracy (88%). Fusing flower frontal, flower lateral and leaf top views yields the most reasonable compromise with respect to acquisition effort and accuracy (96%). The perspective achieving the highest accuracy was species dependent. Conclusions We argue that image databases of herbaceous plants would benefit from multi organ observations, comprising at least the front and lateral perspective of flowers and the leaf top view.

Abstract Background Modern plant taxonomy reflects phylogenetic relationships among taxa based on proposed morphological and genetic similarities. However, taxonomical relation is not necessarily reflected by close overall resemblance, but rather by commonality of very specific morphological characters or similarity on the molecular level. It is an open research question to which extent phylogenetic relations within higher taxonomic levels such as genera and families are reflected by shared visual characters of the constituting species. As a consequence, it is even more questionable whether the taxonomy of plants at these levels can be identified from images using machine learning techniques. Results Whereas previous studies on automated plant identification from images focused on the species level, we investigated classification at higher taxonomic levels such as genera and families. We used images of 1000 plant species that are representative for the flora of Western Europe. We tested how accurate a visual representation of genera and families can be learned from images of their species in order to identify the taxonomy of species included in and excluded from learning. Using natural images with random content, roughly 500 images per species are required for accurate classification. The classification accuracy for 1000 species amounts to 82.2% and increases to 85.9% and 88.4% on genus and family level. Classifying species excluded from training, the accuracy significantly reduces to 38.3% and 38.7% on genus and family level. Excluded species of well represented genera and families can be classified with 67.8% and 52.8% accuracy. Conclusion Our results show that shared visual characters are indeed present at higher taxonomic levels. Most dominantly they are preserved in flowers and leaves, and enable state-of-the-art classification algorithms to learn accurate visual representations of plant genera and families. Given a sufficient amount and composition of training data, we show that this allows for high classification accuracy increasing with the taxonomic level and even facilitating the taxonomic identification of species excluded from the training process.

Abstract Background Phytoplankton species identification and counting is a crucial step of water quality assessment. Especially drinking water reservoirs, bathing and ballast water need to be regularly monitored for harmful species. In times of multiple environmental threats like eutrophication, climate warming and introduction of invasive species more intensive monitoring would be helpful to develop adequate measures. However, traditional methods such as microscopic counting by experts or high throughput flow cytometry based on scattering and fluorescence signals are either too time-consuming or inaccurate for species identification tasks. The combination of high qualitative microscopy with high throughput and latest development in machine learning techniques can overcome this hurdle. Results In this study, image based cytometry was used to collect ~ 47,000 images for brightfield and Chl a fluorescence at 60× magnification for nine common freshwater species of nano- and micro-phytoplankton. A deep neuronal network trained on these images was applied to identify the species and the corresponding life cycle stage during the batch cultivation. The results show the high potential of this approach, where species identity and their respective life cycle stage could be predicted with a high accuracy of 97%. Conclusions These findings could pave the way for reliable and fast phytoplankton species determination of indicator species as a crucial step in water quality assessment.

Abstract Background Predicting a list of plant taxa most likely to be observed at a given geographical location and time is useful for many scenarios in biodiversity informatics. Since efficient plant species identification is impeded mainly by the large number of possible candidate species, providing a shortlist of likely candidates can help significantly expedite the task. Whereas species distribution models heavily rely on geo-referenced occurrence data, such information still remains largely unused for plant taxa identification tools. Results In this paper, we conduct a study on the feasibility of computing a ranked shortlist of plant taxa likely to be encountered by an observer in the field. We use the territory of Germany as case study with a total of 7.62M records of freely available plant presence-absence data and occurrence records for 2.7k plant taxa. We systematically study achievable recommendation quality based on two types of source data: binary presence-absence data and individual occurrence records. Furthermore, we study strategies for aggregating records into a taxa recommendation based on location and date of an observation. Conclusion We evaluate recommendations using 28k geo-referenced and taxa-labeled plant images hosted on the Flickr website as an independent test dataset. Relying on location information from presence-absence data alone results in an average recall of 82%. However, we find that occurrence records are complementary to presence-absence data and using both in combination yields considerably higher recall of 96% along with improved ranking metrics. Ultimately, by reducing the list of candidate taxa by an average of 62%, a spatio-temporal prior can substantially expedite the overall identification problem.

Abstract Background Automated species identification is a long term research subject. Contrary to flowers and fruits, leaves are available throughout most of the year. Offering margin and texture to characterize a species, they are the most studied organ for automated identification. Substantially matured machine learning techniques generate the need for more training data (aka leaf images). Researchers as well as enthusiasts miss guidance on how to acquire suitable training images in an efficient way. Methods In this paper, we systematically study nine image types and three preprocessing strategies. Image types vary in terms of in-situ image recording conditions: perspective, illumination, and background, while the preprocessing strategies compare non-preprocessed, cropped, and segmented images to each other. Per image type-preprocessing combination, we also quantify the manual effort required for their implementation. We extract image features using a convolutional neural network, classify species using the resulting feature vectors and discuss classification accuracy in relation to the required effort per combination. Results The most effective, non-destructive way to record herbaceous leaves is to take an image of the leaf’s top side. We yield the highest classification accuracy using destructive back light images, i.e., holding the plucked leaf against the sky for image acquisition. Cropping the image to the leaf’s boundary substantially improves accuracy, while precise segmentation yields similar accuracy at a substantially higher effort. The permanent use or disuse of a flash light has negligible effects. Imaging the typically stronger textured backside of a leaf does not result in higher accuracy, but notably increases the acquisition cost. Conclusions In conclusion, the way in which leaf images are acquired and preprocessed does have a substantial effect on the accuracy of the classifier trained on them. For the first time, this study provides a systematic guideline allowing researchers to spend available acquisition resources wisely while yielding the optimal classification accuracy.

Current rates of species loss triggered numerous attempts to protect and conserve biodiversity. Species conservation, however, requires species identification skills, a competence obtained through intensive training and experience. Field researchers, land managers, educators, civil servants, and the interested public would greatly benefit from accessible, up-to-date tools automating the process of species identification. Currently, relevant technologies, such as digital cameras, mobile devices, and remote access to databases, are ubiquitously available, accompanied by significant advances in image processing and pattern recognition. The idea of automated species identification is approaching reality. We review the technical status quo on computer vision approaches for plant species identification, highlight the main research challenges to overcome in providing applicable tools, and conclude with a discussion of open and future research thrusts.

Steady improvements of image description methods induced a growing interest in image-based plant species classification, a task vital to the study of biodiversity and ecological sensitivity. Various techniques have been proposed for general object classification over the past years and several of them have already been studied for plant species classification. However, results of these studies are selective in the evaluated steps of a classification pipeline, in the utilized datasets for evaluation, and in the compared baseline methods. No study is available that evaluates the main competing methods for building an image representation on the same datasets allowing for generalized findings regarding flower-based plant species classification. The aim of this paper is to comparatively evaluate methods, method combinations, and their parameters towards classification accuracy. The investigated methods span from detection, extraction, fusion, pooling, to encoding of local features for quantifying shape and color information of flower images. We selected the flower image datasets Oxford Flower 17 and Oxford Flower 102 as well as our own Jena Flower 30 dataset for our experiments. Findings show large differences among the various studied techniques and that their wisely chosen orchestration allows for high accuracies in species classification. We further found that true local feature detectors in combination with advanced encoding methods yield higher classification results at lower computational costs compared to commonly used dense sampling and spatial pooling methods. Color was found to be an indispensable feature for high classification results, especially while preserving spatial correspondence to gray-level features. In result, our study provides a comprehensive overview of competing techniques and the implications of their main parameters for flower-based plant species classification.