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Executive Summary Objectives The objective of EMPHASIS-prep is to develop a long term, distributed, pan-European infrastructure for state-of-the-art plant phenotyping experimental installations, which aims to improve crop performance to cope with climate changes and to keep pace with population growth. Plant researchers are required to test the improvement of plant and crop performance by using all categories of plant phenotyping infrastructures (as described in the deliverable D2.1. criteria list for plant phenotyping infrastructure) which can and should be combined together in a multiscale plant phenotyping approach, ideally, within a coordinated infrastructure, linked with an integrated data management system for storing and analyzing (meta)data, and with modelling platforms associated with the phenotyping platforms. To be able to form this distributed plant phenotyping infrastructure and understand the comparability and/or differences between installations, it is essential to map the new and existing plant phenotyping platforms that uses non-destructive, image-analysis based determination of the phenotype of plants and allow for a characterization of plant traits. This exercise of mapping the infrastructures has been performed and the results can be consulted in the EMPHASIS-PREP deliverable D2.3 mapping of existing and upcoming infrastructures. Deliverable D2.4, extensively describes the analyzing of the gaps and limitations based on the mapping activities. Moreover, where possible, the gaps will be strategically addressed to define how EMPHASIS could be helpful in the future to tackle these gaps in services towards excellence in plant phenotyping science within Europe. Nevertheless, mapping and knowing the limitations of the European situation of the distributed infrastructure is not sufficient to understand the landscape of the experimental phenotyping installations in Europe and its financial impact. Knowing the life cycle of the installations, the time when updates and/or upgrades are needed and the life span before decommissioning of the installations, will complement the understanding of the operation of the installations and allow for planning and interaction between installations on a pan-European level. Rationale This deliverable, describes the analysis of life cycles of plant phenotyping experimental installations which will provide insights in when installations require updates, upgrades, in both software and hardware of the systems, or, as a last step in the life cycle, requires decommissioning. The report summarizes surveys of the way life cycle is currently managed in plant phenotyping installations, in the 5 categories identified in D2.1., on the level of updates and upgrades on hardware systems, implementation of software systems, including an analysis of the financial situation of updates. The results of the deliverable have been obtained by analysis of data from two sources: (1) interviews with 20 different installation managers of European plant phenotyping installations, within countries: The Netherlands, Belgium, France, UK, Germany, Italy and Czech Republic. All interviews have been added within the attachment of this deliverable. ; (2) Survey results of the 2021 survey of IPPN and EMPHASIS, with 396 participants of European origin.During the lifecycle of an infrastructure the costs may vary substantially for example with respect to investment, operation or decommissioning. Within the main results we observe big differences between the different phenotyping categories (see D2.1 Criteria list), updates and upgrades on fields are almost nonexistent, whereas software tools need constant updates and controlled conditions need bigger upgrades every 5 to 10 years. Data about decommissioning was not easy to find as plant phenotyping, with automated systems, is a fairly new branch in plant science.

Executive Summary This deliverable aims at describing the user orientation towards EMPHASIS pilot services. This document provides a summary of the results of the Global Plant Phenotyping Survey launched in November 2020 and concluded in March 2021. GPPS was performed in collaboration with the International Plant Phenotyping Network (IPPN). The plant phenotyping community was interrogated both on general issues and on a set of specific questions to further evaluate EMPHASIS pilot services, which were developed on the basis of the user demand identified by the past two surveys (2017 and 2018). Data collected are a picture of the recent trends in plant phenotyping in Europe and can serve as valuable tools for further analyses to help shaping and supporting the future of plant phenotyping. The database originated from the survey has been delivered to the phenotyping community: https://zenodo.org/badge/DOI/10.5281/zenodo.4723409.svg

Executive Summary Objectives:The improvement of crop performance to address the challenges imposed by climate change and in view of a continuous increases of the world population (and its needs for wellbeing and healthy diet), is a major goal to establish a sustainable agriculture. In this scenario phenotyping is at the forefront of future plant breeding and selection, and the plant phenotyping community must confront with the need to accurately measure diverse traits of an increasingly large number of plants (and genotypes or ecotypes) to successfully address novel challenges beside a sheer rise of plant productivity, such as increasing plants adaptability to resourcelimiting environments and resilience to stress, and successful implementation of low-input agriculture with selected and appropriate plants. Technological advancement is the basis to foster the development of phenotyping centres, while data standardization, acquisition and reusability must be considered as major objectives. Thus, future trends in the development of plant phenotyping need the integration of different experts and disciplines (spanning biological sciences, computer science, mathematics and engineering) with a multidisciplinary view trying to identify a common language, and pipelines to endure a fruitful collaboration between technology developers, providers of infrastructures and increasingly different categories of users. This deliverable gives a snapshot on current EMPHASIS activities, users and stakeholders, and maps existing and future demands of plant phenotyping in order to meet the user expectations towards plant phenotyping infrastructures in a long-term view, facilitating science- and technology-based strategy developments and policies. Rationale:Exploring the user and stakeholder demands is a continues and evolving process that is fundamental for the long-term sustainability of EMPHASIS as a distributed infrastructure. The user demands presented in this deliverable is the result of data acquisition implemented by EMPHASIS-Prep through two surveys launched in 2017 and 2018 to explore the phenotyping community as a whole. The data of the surveys were combined with bibliographic sources, by means of a bibliographic analysis to measure the phenotyping scientific production, research and trends, and that was taken into account to draw the current and future user demands. The future demand for plant phenotyping also considered the burning necessity to efficiently integrate the different communities involved in plant phenotyping, here defined as plant phenotyping integration process. Main results:To define the current and future user demands, we identified the EMPHASIS users, and mapped the demand accordingly to the following categorization: Demand for phenotyping in general; Demand for access to infrastructures and data; Demand for innovation; Demand for training; Demand for modelling. From this analysis it emerges: 1) an increasing demand for training, especially keyed at training for imaging and bioinformatics; 2) an increased demand for access the phenotyping infrastructures 3) the need of a even wider and more integrated community to address phenotyping challenges and foster complementation across different disciplines. &nbsp

Executive Summary Objectives In its preparatory phase (EMPHASIS-PREP), the EMPHASIS project will develop a long-term sustainable strategy for the user-driven building, upgrading and operation of plant phenotyping infrastructures. This deliverable deals with the definition of a criteria list to describeuser demand with respect to EMPHASIS plant phenotyping infrastructures (RIs) and resulting services as well as different access modes to infrastructure and services. A criteria list for user demand is functional tothe description of users requesting access to EMPHASIS infrastructures and services, and of the scopes for which access isrequested. The deliverable is essential to provide concrete benefits to the community, and to help shaping the EMPHASIS-PREP catalogue of services. The criteria list was developed after analysing the result of the EMPHASIS survey launched in 2018 by WP3 and WP2, concerning the mapping of users, of user demand and of the different access mode. This information was then matched with the list of infrastructures previously identified in deliverable 2.1, elaborated by WP2. Main Results The data collected by the 2018 survey “Do you need plant phenotyping?”were analysed to identify: a) the users involved/interested in EMPHASIS, b) their demands, and c) their expectations and needs towards EMPHASIS. A large fraction of the participants in the survey werefrom the scientific community, which showed to be highly interested in the phenotyping opportunities offered by EMPHASIS-PREP.Twenty percent of the participants were from private companies,showing rising industrial interest in plant phenotyping. For most of the participants EMPHASIS-PREP should support training in plant phenotyping and the expansion of theirresearch network. In 47% of the cases the request was for access to installations. On the basis of user demand towards the EMPHASIS–PREP infrastructures a criteria list was defined for the following types of access and services: ACCESS: access provision for user community to the phenotyping installations incl.: controlled environment installations, field installations, networks of field sites, modelling. QUALITY: measures to implement quality criteria at research infrastructure, specifically experimental design, standards, sensor calibration etc. DATA MANAGEMENT: approaches enabling data reusability embedded in a relevant data policy. INNOVATION: dissemination and utilization of technology and results from access and use of the phenotyping installations. COMMUNICATION: engaging all relevant stakeholders. TRAINIG: supporting the next generation of plant scientist. EXPERT ADVICE: assessment of the plant phenotyping landscape specifically to funders and decision makers

n the original article, the reference for the "European Biostimulant Industry Council" was incorrectly written as "(Electron-Beam-Induced Current [EBIC, 2018])". It should be "(EBIC, 2018)." The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.

Executive Summary Objectives: Europe is at the forefront of research on plant phenotyping. Some of the best infrastructures for plant phenotyping are based on laboratories and platforms leaded by European institutions. The development of a more structured and interconnected phenotyping community allowing the implementation of the infrastructures, enhancing the access is one of the major objective of EMPHASIS. However, to bridge the gap between crop phenotyping and the rich array of refined genomic already available, we need to train a new generation of researchers who can undertake, develop and exploit phenotyping technologies, interpreting multidimensional phenomic data required to address current and future challenges in agriculture and plant science, namely how to feed the world, sustainably use natural resources, and contribute to the bio economy. Rationale: A number of education and training activities on phenotyping are currently already performed at European and International level. Nevertheless, these still remain stand-alone and one-off initiatives, which require a further degree of structuring and integration. Mapping of ongoing or foregoing training activities in plant phenotyping is a mandatory exercise to fill the gaps. In 2017, some analysis were performed by WP3 in collaboration with other WPs to map the state-of-the art of plant phenotyping training activities through: i) regional mapping Conferences; ii) the 2017 survey addressed to the plant phenotyping community and iii) internet- based research. Main Results: From the mapping of training activities, an increased need of training is emerging especially in data management. For this reason, a more coordinated action is necessary to offer all the interested stakeholder adequate training instruments to disseminate the plant phenotyping knowledge among the identified target groups.