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The NanoDefine Methods Manual has been developed within the NanoDefine project 'Development of an integrated approach based on validated and standardized methods to support the implementation of the EC recommendation for a definition of nanomaterial', funded by the European Union's 7th Framework Programme, under grant agreement 604347. The overall goal of the NanoDefine project was to support the implementation of the European Commission Recommendation on the definition of nanomaterial (2011/696/EU). The project has developed an integrated empirical approach, which allows identifying a material as a nano- or not a nanomaterial according to the EC Recommendation. The EC Recommendation for a definition of nanomaterial provides a common basis for regulatory purposes across all areas of European Union policy. The definition or core parts of it have been enacted in EU legislation, (e.g. REACH, Biocidal Products Regulation, Medical Devices Regulation). Therefore, development of appropriate methods and approaches to understand if a material meets the criteria laid down in the EC NM Definition is of key importance for both industry, stakeholders and regulators. The NanoDefine Methods Manual aims at providing guidance through the nanomaterial characterization process, on the use of the characterization methods as well as their application range and their limits to assists the user in choosing the most appropriate measurement method(s) to identify any substance according to the EC recommendation for a definition of nanomaterial. The NanoDefine Methods Manual consists of three parts. Part 1: covers the NanoDefiner framework. It includes short introduction to the NanoDefine Framework and summarizes the results of a comprehensive study of the available Characterisation Methods (CMs) which were candidates for a reliable analysis of the number based size distribution of a particulate material, with the goal to identify nanomaterials according to the EC NM Definition. The report presents the Decision Support Flow Scheme, which guides the user logically through a sequence of tasks, decision nodes and options in order to decide whether a material is a nanomaterial according to the EC NM Definition. Finally the report introduce the NanoDefiner e–tool which implements all tools developed within the NanoDefine framework in a software and assists the user in the decision process whether a material is a nanomaterial according to the EC NM Definition. Part 2: discusses the outcome of the evaluation of the nanomaterials characterisation methods. The document is based on the results of a comprehensive study performed within the NanoDefine project on the available Characterisation Methods (CMs) which are candidates for performing a reliable analysis of the number-based size distribution of a particulate material, with the goal to identify nanomaterials according to the European Commission recommendation on the definition of nanomaterial. This report discusses most available size characterisation methods for nanomaterials. Different types of methods that allow for the determination of size and size distributions are described and an overview of techniques and their capabilities is presented in the form of detailed, user-friendly tables. Part 3: gathers all Standard Operating Procedures (SOPs) developed within the NanoDefine project (available at the editorial deadline of the Manual) for nanomaterial characterisation. The aim of this document is to present SOPs developed within NanoDefine project to facilitated and harmonised the particle size distribution measurements. The presented SOPs are detailed, material/method specific protocols designed to produce liquid dispersions of the NanoDefine priority substances such that the resulting dispersions are stable and contain only or mainly primary constituent particles. All SOPs are presented in the document as standalone, self-explanatory documents which then can be easily extracted from the report. Special attention is given to the sonication issue, as it seems to be one of the most challenging steps in the sample preparation. The NanoDefine Methods Manual is available in a form of three separated Reports or in a special format of a full collection.