F°Low : EM goes FAIR. A novel database software to track with high accuracy the journey of a biological sample towards electron microscopy analysis.

F°Low : EM goes FAIR. A novel database software to track with high accuracy the journey of a biological sample towards electron microscopy analysis. | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Resource F°Low : EM goes FAIR. A novel database software to track with high accuracy the journey of a biological sample towards electron microscopy analysis. Xavier Heiligenstein, Martin Belle This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4133153/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Electron microscopy (EM) plays a crucial role in biological research, yet its widespread adoption is hindered by the lack of standardized protocols and efficient workflow management. This study addresses this challenge by introducing F°Low, a novel software solution designed to streamline the tracking and management of individual experiments in EM sample preparation. We highlight its focus on project management, sample tracking, and protocol refinement. F°Low prioritizes adherence to FAIR principles and facilitates knowledge transmission by providing a user-friendly interface for experiment creation and management. By standardizing the tracking process and promoting protocol improvement from the outset, F°Low aims to transmit EM expertise and enhance efficiency in biological research. Biological sciences/Biological techniques/Software Scientific community and society/Scientific community/Research management Scientific community and society/Business and industry/Industry Scientific community and society/Scientific community/Research data/Databases Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Introduction Electron microscopy (EM) has emerged as an indispensable tool in biological research, offering unprecedented insights into the intricate structures and dynamics of biological specimens. Despite its versatility across various sample types and imaging methods, the workflow of EM traditionally follows a linear trajectory: from live material to fixed, vacuum-shielded specimens, thinning, ultimately culminating in observation. However, within this trajectory lie numerous intermediate steps and imaging processes, essential for tracking sample modifications or evolutions. This journey often converges into the realm of correlative light and electron microscopy (CLEM), where multiple imaging modalities intersect to provide a comprehensive understanding of biological samples. Establishing an electron microscopy facility at the INSERM Unit U1195 in le Kremlin-Bicêtre, France, revealed the prevalent challenge of efficiently tracking multiple samples across diverse projects. While laboratory notebooks have served as the backbone of sample documentation for decades, their utilization lacks standardization, posing significant hurdles in data accessibility and continuity, particularly upon personnel turnover. The advent of Electronic Lab Notebooks (ELNs) presents a modern solution to streamline project tracking and data management. In our experience, navigating through EM samples from various users became increasingly arduous without a systematic approach. This led to the development of a comprehensive tracking system, meticulously documenting each EM bloc in an expanding Excel spreadsheet managed by our lab personnel. This entailed identifying group leaders, projects, experiments, unique samples, and their respective transformations, alongside associated metadata. Notably, for CLEM projects, images captured at intermediate steps further enriched the dataset. The introduction of unique sample identification numbers enhanced sample findability, critical for project completion and long-term data accessibility. Leveraging a structured subfolder template for data organization facilitated efficient data retrieval and mining, ensuring the accessibility of physical data across the facility. Moreover, with the facility's involvement in scientific publications, delivering coherent reports at project completion enhanced project interoperability, bridging the gap between facility management and sample preparation teams. Attaching the report as a supplementary data in publications would also more effectively standardize the transmission of protocols across laboratories. To address the aforementioned challenges comprehensively, we introduce F°Low, a novel database management tool tailored specifically for electron microscopy projects. Structured as a facility management platform, F°Low enables the creation of group leader pages, independent projects, and experiment sets. By estimating equipment costs upfront and systematically documenting each sample transformation step with metadata and illustrations, F°Low streamlines project management and enhances data reusability. Filling F°Low along the stream of data is facilitated by a structured interface, by copy-pasting images or recipe, duplicating samples or typing individual comments. Pre-existing excel data sheet can be imported to ensure seamless transition. The automatically generated PDF summary serve as identification cards, facilitating supplementary data sharing and reinforcing the FAIR principles (Findable, Accessible, Interoperable, and Reusable) in EM data management. In summary, F°Low represents a pivotal advancement in centralizing and standardizing EM data management, offering a robust solution for protocol dissemination and knowledge transfer within the scientific community. Results Administration and Access Control in F°Low: F°Low is designed to serve as a centralized platform for managing electron microscopy (EM) samples across diverse projects within a facility. To ensure efficient operation and data security, the system incorporates hierarchical levels of authorization, delineating responsibilities and access rights for different user roles. The following outlines the specific privileges granted to each user category: 1. Facility Manager: Manage equipment inventory, including assigning equipment to workflow steps and defining usage units and costs. Create and manage user groups, comprising facility members, and regulate individual access privileges. Initiate and oversee projects and experiments. Generate quotations and invoices for project-related services. 2. Group Leader: Oversee all projects within their designated group. Appoint administrators within the group to assist in management tasks. Create projects, assign users and visitors, and manage access privileges within the group. Edit project data and access experiment invoices. 3. Administrator (Group Member): Enjoy the same privileges as the group leader, excluding the authority to appoint other administrators. 4. User: Create multiple experiments within associated projects. Specify the working folder for storing experiment data (e.g., local drive, external drive, cloud) and establish the storage architecture. Populate experiment details and progress information. 5. Visitor: Access and view all experiments associated with their profile. Print experiment reports for reference purposes. These distinct user roles and associated permissions ensure streamlined management, data integrity, and controlled access within the F°Low platform. By tailoring privileges to specific responsibilities and expertise levels, the system optimizes collaboration and transparency across project teams while safeguarding sensitive data. Table 1 privilege table to access the database Facility manager group leader administrator user visitor add equipment to workflow steps x define usage and cost x create new group x add members x x x nominate administrators within the group x x administrate authorization (user/visitor) x x x create a project within a group x x x x assign user to a project x x x create an experiment within a project x x x x Inform the path to the working folder and generate the storage architecture x x x x add data to an experiment x x x x read an experiment x x x x x print and experiment report x x x x x see and print invoice x x x Equipment Setup in F°Low: In F°Low, the facility manager possesses exclusive access to a designated page termed "parameters", facilitating the seamless association of equipment with predefined workflow steps essential for sample preparation in electron microscopy (EM) projects. These steps encompass a comprehensive range of processes from sample immobilization to final imaging, ensuring coverage of the most common sample preparation procedures encountered in biological research. The predefined steps within F°Low include: Sample Immobilization: Chemical fixation, Plunge freezing, High-pressure freezing Cryo Light Microscopy Dehydration – Embedding / Freeze-substitution In-Resin Fluorescence Ultramicrotomy – Thinning On-section Light Microscopy Electron Microscopy CLEM Registration (Correlative Light and Electron Microscopy) Other The inclusion of these steps reflects a comprehensive approach to sample preparation, spanning from live specimen handling to advanced EM imaging techniques. The facility manager is empowered to populate each step with relevant equipment or products, tailoring the setup to the specific requirements and resources of the facility. Furthermore, the manager can assign a cost per unit, room, session, or hour to each equipment entry, thereby facilitating accurate cost estimation for experiments conducted within the facility. These cost estimates play a pivotal role in determining the overall expense associated with a particular experiment, enabling the generation of invoices in alignment with the facility's internal charging policy. The granularity of cost breakdown is customizable within each facility, reflecting its unique operational structure and financial considerations. By integrating equipment setup and cost estimation functionalities within F°Low, the platform streamlines project management, enhances financial transparency, and ensures efficient resource allocation within electron microscopy facilities. This integrated approach fosters accountability and optimization, ultimately facilitating the execution of high-quality research endeavors. Creating Projects and Associated Experiments in F°Low: Upon accessing the group leader page, users are presented with their entitled projects, as determined by affiliations established by the group leader or administrators. Each project within F°Low is a structured collection of experiment sets, facilitating organized management and tracking of research endeavors. To initiate an experiment within a project, the user begins by assigning a name to the experiment and specifying a starting date. Subsequently, the user proceeds to create the experiment structure, which involves subdividing it into several sequential steps, each necessitating a specific set of apparatus for execution. Planning experiments within F°Low entails selecting a step from the experiment structure and associating the appropriate equipment, along with entering expected volume and date of use (optional). Acknowledging the potential variance between anticipated and actual time investments, users have the flexibility to update the actual volume expended, enabling recalibration of the final cost estimation for the experiment. Integral to this process is the specification of the "work folder path" where future experiment data will be stored. This feature ensures long-term sample traceability, even years after project initiation, mitigating the risk of data loss and facilitating data retrieval for subsequent analyses or reference. Additionally, users are encouraged to provide contextual “comments” on the project, enhancing understanding of the experiment's objectives and significance. Upon completion or update, users have the option to populate the experiment with relevant data sections or navigate to it if the experiment already exists within the system. This streamlined workflow in F°Low empowers researchers to efficiently manage and execute their experiments while promoting data integrity and accessibility throughout the project lifecycle. Experiment Management in F°Low: The experiment page within F°Low comprises three main areas designed to streamline experiment organization and execution, ensuring comprehensive tracking and documentation of sample transformations: 1. Navigation Panel: Located at the top row, this panel enables quick navigation between the group leader, project, and individual experiments, facilitating seamless access to pertinent information. 2. Experiment Structure: The left column is divided into two sections: The top section presents the predefined steps established during experiment creation, logically ordered from live sample handling to correlative light and electron microscopy (CLEM), enabling a chronological overview of sample processing. The bottom section lists the samples contained within the specific experiment, allowing for comparative analysis of sample evolution across different steps. 3. Central Information Panel: The central section of the experiment page provides detailed information on the consulted step, offering insights into key procedures and considerations: A. Sample Fixation/Vitrification: Provides a comprehensive overview of the fixation/vitrification process, including pre-fixation conditions and the vitrification method if conducted during the experiment. Allows insertion of images captured before immobilization (Heiligenstein et al., 2021; Koning et al., 2014, 2022) and diagrams illustrating the high-pressure freezing (HPF) protocol. Offers a spacious commentary area to document diverse fixation approaches, sample characteristics, and preparation details. B. Cryo Light Microscopy: Allows inclusion of representative images to depict this step, aiding in visualizing experimental outcomes. Provides space for user comments and annotations for enhanced documentation. C. Freeze-Substitution/Staining/Dehydration/Embedding: Acknowledges the complexity and duration of the freeze-substitution process, often involving multiple samples across various experiments (supplementary Fig. 1). Facilitates creation and application of freeze-substitution (FS) protocols to multiple independent experiments, streamlining workflow efficiency. Supports both conventional chemical fixation and FS procedures, accommodating diverse experimental protocols and approaches. Each step can be detailed precisely in temperature, temperature ramp, time, reagents and solvents. This table form may be imported or exported in a CSV format. Template may therefore be used to speed-up the completion time and adjusted to each batch if necessary. D. In-Resin Fluorescence Microscopy: Offers provision for inclusion of representative images for visual illustration. Encourages user input through comments and annotations to enrich experiment documentation. Here, the acquisition metadata are inserted in the manufacturer proprietary format for later reuse. E. Ultramicrotomy: Ensures compliance with FAIR principles by enabling storage box linkage for EM grids post-experiment. Facilitates efficient organization and labelling of storage boxes, enhancing long-term sample traceability. Supports Tokuyasu immunolabeling assignment to individual EM grids, enabling precise tracking of labelling trials. The box table may be printed to be completed at the bench. F. On-Section Microscopy: Provides space for representative images and user comments, enhancing documentation clarity and completeness. Comparable to Cryo Light Microscopy, In Resin Microscopy. This section applies particularly to ‘on section fluorescence microscopy’ or ‘array tomography’ approaches. G. Electron Microscopy: Allows inclusion of representative images and user comments for comprehensive experiment documentation. H. CLEM Registration: Facilitates illustration of the CLEM workflow through representative images from light microscopy, electron microscopy, and CLEM stages. Offers space for user comments to capture additional insights and observations. This centralized information panel serves as a comprehensive repository for documenting experiment details, ensuring clarity, reproducibility, and adherence to FAIR principles in electron microscopy research. Data Organization: F°Low promotes adherence to FAIR principles by recommending a predetermined folder architecture within the experiment folder, ensuring long-term findability of experiment data. This architecture includes folders for live data, curve data, block data, SEM images, TEM images, and image analysis results, or a similar structure validated by the working environment. It embraces a broad perspective, that may target the user to more dedicated metadata generated by each apparatus used in the protocol. Experiment Report Sharing: To facilitate experiment exploration and report transmission, F°Low enables the printing of a concise 2-page PDF summary of the experiment (supplementary file 1). This summary can be stored at the root of the sample and shared with collaborators or stakeholders. Internally, physical samples are affixed to printed PDF summaries, creating accurate time stamps for each sample and eliminating untraceable sample blocks. By integrating these features, F°Low enhances experiment management, documentation, and sharing, promoting transparency, reproducibility, and efficiency in electron microscopy research endeavors. Discussion Electron microscopy (EM) remains a cornerstone technique in biological research, offering unparalleled resolution and insight into cellular structures and dynamics. However, despite its established utility, the adoption of EM is hindered by several challenges, perpetuating a perception of high expertise requirements and hindering widespread utilization. Several publications point out to the data management, in the perspective of the large volume generated (Poger et al., 2023; Rzepka et al., 2023). We acknowledge this challenge, but focus more on the detailed transformation of the sample, undertaking variable but predictable pathways. One significant challenge lies in the lack of standardized protocols for sample preparation, leading to a fragmented and artisanal approach to EM. The absence of streamlined protocols makes it daunting for scientists to navigate the intricate pathways from live samples to EM imaging. As a result, accessing precise protocols often entails contacting authors directly or relying on non-standardized documentation, impeding efficient knowledge transfer within and across research laboratories. Exploring existing solutions in the field, we identified several software offerings aiming to address aspects of EM workflow management. ThermoFisherScientific's Athena Software and PPMS from Stratocore focus primarily on image analysis and resource management, respectively, but lack comprehensive support for project management and sample tracking from an individual user perspective. Similarly, the EMPIAR database's Sample Preparation Widget aims to synthesize complex workflows but falls short in tracking individual samples and facilitating routine experiment management. In contrast, our solution, F°Low, emphasizes the standardization and tracking of individual experiments, aligning closely with the FAIR principles (Findable, Accessible, Interoperable, and Reusable). By providing a user-friendly interface for creating and managing experiments, F°Low streamlines the sample preparation process and enhances knowledge transmission within research teams. Unlike existing solutions, F°Low prioritizes the identification of appropriate samples and the iterative improvement of protocols through a systematic and synthetic overview from the outset of the experiment. In conclusion, while existing Data Management software solutions offer valuable contributions to resource management and reporting, F°Low distinguishes itself by focusing on individual experiment tracking and protocol refinement. By standardizing the tracking process and promoting adherence to FAIR principles, F°Low represents a significant step towards democratizing EM and fostering efficient knowledge transmission in biological research. References Heiligenstein, X., de Beer, M., Heiligenstein, J., Eyraud, F., Manet, L., Schmitt, F., Lamers, E., Lindenau, J., Kea-te Lindert, M., Salamero, J., Raposo, G., Sommerdijk, N., Belle, M., & Akiva, A. (2021). HPM live μ for a full CLEM workflow (pp. 115–149). https://doi.org/10.1016/bs.mcb.2020.10.022 Koning, R. I., Faas, F. G., Boonekamp, M., de Visser, B., Janse, J., Wiegant, J. C., de Breij, A., Willemse, J., Nibbering, P. H., Tanke, H. J., & Koster, A. J. (2014). MAVIS: an integrated system for live microscopy and vitrification. Ultramicroscopy , 143 , 67–76. https://doi.org/10.1016/j.ultramic.2013.10.007 Koning, R. I., Vader, H., van Nugteren, M., Grocutt, P. A., Yang, W., Renault, L. L. R., Koster, A. J., Kamp, A. C. F., & Schwertner, M. (2022). Automated vitrification of cryo-EM samples with controllable sample thickness using suction and real-time optical inspection. Nature Communications 2022 13:1 , 13 (1), 1–10. https://doi.org/10.1038/s41467-022-30562-7 Poger, D., Yen, L., & Braet, F. (2023). Big data in contemporary electron microscopy: challenges and opportunities in data transfer, compute and management . 160 , 169–192. https://doi.org/10.1007/s00418-023-02191-8 Rzepka, N., Bogovic, J. A., & Moore, J. A. (2023). Toward scalable reuse of vEM data: OME-Zarr to the rescue. Methods in Cell Biology , 177 , 359–387. https://doi.org/10.1016/BS.MCB.2023.01.016 Additional Declarations Yes there is potential Competing Interest. CryoCapCell imagined, developped and commercialize research tools. F°Low is licensed by CryoCapCell. Supplementary Files Supplementary1HighresolutionstageHPF06CC06.pdf SummaryForm SupplementaryFigure1.jpg Supplementary figure 1: The batch processing of dehydration/embedding/freeze-substitution is prepared in a separate Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4133153","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Resource","associatedPublications":[],"authors":[{"id":281968004,"identity":"0ccaba49-e6a4-4707-a829-b471b29bf214","order_by":0,"name":"Xavier Heiligenstein","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA50lEQVRIie3PsQqCQBjA8U8OdKmuUYnyFZSglvBZLg6cfIcCwal2g54jGhq+w6FFag0aA7dAt4KCrAYnzbag+w/HfXA/7g5AJvvREGBUTC2tHnGLSSX1Loq+INY2tjHb7M1hyEV6XTu9nChp5pUTY+ZZIkyO9vLgcmMe835OiLFYlRMKLosaeGS67g2gGeA4IPnbmhVEpQmLbrh7EeUe4OQjoTrHCBBfhOS3MPUTMcITihlyO2wkvNONuR0Qxa/8i7Uf++kFHVPXuMjOa8ekmi/SrIIUtRmAMn3u3muNKH5xWCaTyf6qByOKTV6VuaoqAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0003-4006-2639","institution":"CryoCapCell","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Xavier","middleName":"","lastName":"Heiligenstein","suffix":""},{"id":281968005,"identity":"caff7e9a-c067-4517-be69-9bda77910c70","order_by":1,"name":"Martin Belle","email":"","orcid":"","institution":"CryoCapCell","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Martin","middleName":"","lastName":"Belle","suffix":""}],"badges":[],"createdAt":"2024-03-19 23:20:41","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4133153/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4133153/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":53192177,"identity":"f3f19c74-4ede-45af-9d7e-1017fb63d206","added_by":"auto","created_at":"2024-03-21 17:46:51","extension":"jpg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":179869,"visible":true,"origin":"","legend":"\u003cp\u003econstruct experiment backbone, estimate time and cost, and compare to time actually spent. Inform the work folder (mandatory) and explain in a few sentences the objective of the experiment (optional).\u003c/p\u003e","description":"","filename":"Figure1.jpg","url":"https://assets-eu.researchsquare.com/files/rs-4133153/v1/778b939accd68b55074ab729.jpg"},{"id":53191663,"identity":"c84a37f3-d681-4787-ab9e-4e1c764d855a","added_by":"auto","created_at":"2024-03-21 17:38:51","extension":"jpg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":134559,"visible":true,"origin":"","legend":"\u003cp\u003efixation page, representative images of the sample prior to fixation, sample name and type, date of immobilization. Adaptable to chemical fixation, plunge freezing and high pressure freezing.\u003c/p\u003e","description":"","filename":"Figure2.jpg","url":"https://assets-eu.researchsquare.com/files/rs-4133153/v1/396db2cf65d19ec959224bb6.jpg"},{"id":53191668,"identity":"c9d50f7c-933e-40bd-a6c2-9f32f51d69dc","added_by":"auto","created_at":"2024-03-21 17:38:51","extension":"jpg","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":169606,"visible":true,"origin":"","legend":"\u003cp\u003efreeze-substitution/dehydration/embedding page. This page is selected from the list of experiment created under the Freeze-substitution page. It cannot be edited from the sample page as this process is done in batches. From the Freeze-substitution page, all samples that composed the batch are listed (supplementary figure 1). The primary fixation cocktail is detailed, the main solvent and final embedding substrate is highlighted. For each step number, temperature, slope, duration, reagent and solvent proportions are described. A specific frame may be used to present the measured temperature curve if different from the initial program. Comments may be added.\u003c/p\u003e","description":"","filename":"Figure3.jpg","url":"https://assets-eu.researchsquare.com/files/rs-4133153/v1/b9bcab43962d6fda86227cb4.jpg"},{"id":53191667,"identity":"a84ee786-163a-4219-ae35-73c68cd5eceb","added_by":"auto","created_at":"2024-03-21 17:38:51","extension":"jpg","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":127665,"visible":true,"origin":"","legend":"\u003cp\u003eIn Resin Microscopy page. Similar to other singular imaging steps (cryo Light Microscopy, IRF or Soft X-ray, Electron microscopy), a representative image from the step may be documented with dedicated comments.\u003c/p\u003e","description":"","filename":"Figure4.jpg","url":"https://assets-eu.researchsquare.com/files/rs-4133153/v1/f8c0bbedd4b963f151c21b21.jpg"},{"id":53192178,"identity":"eab675e7-0583-463e-9fb2-76750b706940","added_by":"auto","created_at":"2024-03-21 17:46:51","extension":"jpg","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":164321,"visible":true,"origin":"","legend":"\u003cp\u003eUltramicrotomy page. Ultramicrotomy is a step that splits one single sample into multiple coherent samples. If serially collected, these samples can be serially imaged to generate a volume dataset. The sections might be collected on EM grids or on wafers of various sizes. The order must be accurately tracked to ensure coherent volume reconstruction. An EM grid box may contain several samples from various experiments.\u003c/p\u003e","description":"","filename":"Figure5.jpg","url":"https://assets-eu.researchsquare.com/files/rs-4133153/v1/5c5760173a08a9449b4c033c.jpg"},{"id":53191664,"identity":"13d88889-9ffc-4e0f-90af-26828ce1adf6","added_by":"auto","created_at":"2024-03-21 17:38:51","extension":"jpg","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":110097,"visible":true,"origin":"","legend":"\u003cp\u003eElectron Microscopy. Images, representative of the EM acquisition may be represented. Here, SEM (left, ITO Glass C8) and TEM (right, slot grid B8) images from the sample observed live on the CryoCapsule and then in the Resin Bloc, are presented. The shape is coherent with the live dataset.\u003c/p\u003e","description":"","filename":"Figure6.jpg","url":"https://assets-eu.researchsquare.com/files/rs-4133153/v1/7271569b879b9009f653b33d.jpg"},{"id":53191666,"identity":"0b46fe55-ef13-451f-b465-822180fcabb4","added_by":"auto","created_at":"2024-03-21 17:38:51","extension":"jpg","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":117186,"visible":true,"origin":"","legend":"\u003cp\u003eCLEM registration page. Images from both light and electron microscopy and their registered outcome are presented.\u003c/p\u003e","description":"","filename":"Figure7.jpg","url":"https://assets-eu.researchsquare.com/files/rs-4133153/v1/1eb168ff1c124ad4aa59d31f.jpg"},{"id":53426305,"identity":"0ad09282-1095-4df5-8ab4-504e45348146","added_by":"auto","created_at":"2024-03-25 20:35:30","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":868861,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4133153/v1/d776466b-abd3-4db0-9c91-50a95f5f307e.pdf"},{"id":53191670,"identity":"cca20cea-33e1-4255-99cc-2fdb5aa452c4","added_by":"auto","created_at":"2024-03-21 17:38:51","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":7237182,"visible":true,"origin":"","legend":"\u003cp\u003eSummaryForm\u003c/p\u003e","description":"","filename":"Supplementary1HighresolutionstageHPF06CC06.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4133153/v1/01d5ebb0105d279513847002.pdf"},{"id":53191661,"identity":"3cdcd823-d3b0-4e55-839b-77cb53f37518","added_by":"auto","created_at":"2024-03-21 17:38:51","extension":"jpg","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":160861,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary figure 1: The batch processing of dehydration/embedding/freeze-substitution is prepared in a separate\u003c/p\u003e","description":"","filename":"SupplementaryFigure1.jpg","url":"https://assets-eu.researchsquare.com/files/rs-4133153/v1/bf75dd1c6ca09049e58e4290.jpg"}],"financialInterests":"\u003cb\u003eYes\u003c/b\u003e there is potential Competing Interest.\nCryoCapCell imagined, developped and commercialize research tools. F°Low is licensed by CryoCapCell.","formattedTitle":"F°Low : EM goes FAIR. A novel database software to track with high accuracy the journey of a biological sample towards electron microscopy analysis.","fulltext":[{"header":"Introduction","content":"\u003cp\u003eElectron microscopy (EM) has emerged as an indispensable tool in biological research, offering unprecedented insights into the intricate structures and dynamics of biological specimens. Despite its versatility across various sample types and imaging methods, the workflow of EM traditionally follows a linear trajectory: from live material to fixed, vacuum-shielded specimens, thinning, ultimately culminating in observation. However, within this trajectory lie numerous intermediate steps and imaging processes, essential for tracking sample modifications or evolutions. This journey often converges into the realm of correlative light and electron microscopy (CLEM), where multiple imaging modalities intersect to provide a comprehensive understanding of biological samples.\u003c/p\u003e \u003cp\u003eEstablishing an electron microscopy facility at the INSERM Unit U1195 in le Kremlin-Bic\u0026ecirc;tre, France, revealed the prevalent challenge of efficiently tracking multiple samples across diverse projects. While laboratory notebooks have served as the backbone of sample documentation for decades, their utilization lacks standardization, posing significant hurdles in data accessibility and continuity, particularly upon personnel turnover. The advent of Electronic Lab Notebooks (ELNs) presents a modern solution to streamline project tracking and data management.\u003c/p\u003e \u003cp\u003eIn our experience, navigating through EM samples from various users became increasingly arduous without a systematic approach. This led to the development of a comprehensive tracking system, meticulously documenting each EM bloc in an expanding Excel spreadsheet managed by our lab personnel. This entailed identifying group leaders, projects, experiments, unique samples, and their respective transformations, alongside associated metadata. Notably, for CLEM projects, images captured at intermediate steps further enriched the dataset.\u003c/p\u003e \u003cp\u003eThe introduction of unique sample identification numbers enhanced sample findability, critical for project completion and long-term data accessibility. Leveraging a structured subfolder template for data organization facilitated efficient data retrieval and mining, ensuring the accessibility of physical data across the facility. Moreover, with the facility's involvement in scientific publications, delivering coherent reports at project completion enhanced project interoperability, bridging the gap between facility management and sample preparation teams. Attaching the report as a supplementary data in publications would also more effectively standardize the transmission of protocols across laboratories.\u003c/p\u003e \u003cp\u003eTo address the aforementioned challenges comprehensively, we introduce F\u0026deg;Low, a novel database management tool tailored specifically for electron microscopy projects. Structured as a facility management platform, F\u0026deg;Low enables the creation of group leader pages, independent projects, and experiment sets. By estimating equipment costs upfront and systematically documenting each sample transformation step with metadata and illustrations, F\u0026deg;Low streamlines project management and enhances data reusability.\u003c/p\u003e \u003cp\u003eFilling F\u0026deg;Low along the stream of data is facilitated by a structured interface, by copy-pasting images or recipe, duplicating samples or typing individual comments. Pre-existing excel data sheet can be imported to ensure seamless transition.\u003c/p\u003e \u003cp\u003eThe automatically generated PDF summary serve as identification cards, facilitating supplementary data sharing and reinforcing the FAIR principles (Findable, Accessible, Interoperable, and Reusable) in EM data management.\u003c/p\u003e \u003cp\u003eIn summary, F\u0026deg;Low represents a pivotal advancement in centralizing and standardizing EM data management, offering a robust solution for protocol dissemination and knowledge transfer within the scientific community.\u003c/p\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec4\" class=\"Section2\"\u003e\n\u003ch2\u003eAdministration and Access Control in F\u0026deg;Low:\u003c/h2\u003e\n\u003cp\u003eF\u0026deg;Low is designed to serve as a centralized platform for managing electron microscopy (EM) samples across diverse projects within a facility. To ensure efficient operation and data security, the system incorporates hierarchical levels of authorization, delineating responsibilities and access rights for different user roles. The following outlines the specific privileges granted to each user category:\u003c/p\u003e\n\u003cp\u003e1. Facility Manager:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eManage equipment inventory, including assigning equipment to workflow steps and defining usage units and costs.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eCreate and manage user groups, comprising facility members, and regulate individual access privileges.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eInitiate and oversee projects and experiments.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eGenerate quotations and invoices for project-related services.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003e2. Group Leader:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eOversee all projects within their designated group.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eAppoint administrators within the group to assist in management tasks.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eCreate projects, assign users and visitors, and manage access privileges within the group.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eEdit project data and access experiment invoices.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003e3. Administrator (Group Member):\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eEnjoy the same privileges as the group leader, excluding the authority to appoint other administrators.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003e4. User:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eCreate multiple experiments within associated projects.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eSpecify the working folder for storing experiment data (e.g., local drive, external drive, cloud) and establish the storage architecture.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003ePopulate experiment details and progress information.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003e5. Visitor:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eAccess and view all experiments associated with their profile.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003ePrint experiment reports for reference purposes.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eThese distinct user roles and associated permissions ensure streamlined management, data integrity, and controlled access within the F\u0026deg;Low platform. By tailoring privileges to specific responsibilities and expertise levels, the system optimizes collaboration and transparency across project teams while safeguarding sensitive data.\u003c/p\u003e\n\u003cdiv class=\"gridtable\"\u003e\n\u003ctable id=\"Tab1\" border=\"1\"\u003e\u003ccaption\u003e\n\u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e\n\u003cdiv class=\"CaptionContent\"\u003e\n\u003cp\u003eprivilege table to access the database\u003c/p\u003e\n\u003c/div\u003e\n\u003c/caption\u003e\n\u003cthead\u003e\n\u003ctr\u003e\n\u003cth align=\"left\"\u003e\u0026nbsp;\u003c/th\u003e\n\u003cth align=\"left\"\u003e\n\u003cp\u003eFacility manager\u003c/p\u003e\n\u003c/th\u003e\n\u003cth align=\"left\"\u003e\n\u003cp\u003egroup leader\u003c/p\u003e\n\u003c/th\u003e\n\u003cth align=\"left\"\u003e\n\u003cp\u003eadministrator\u003c/p\u003e\n\u003c/th\u003e\n\u003cth align=\"left\"\u003e\n\u003cp\u003euser\u003c/p\u003e\n\u003c/th\u003e\n\u003cth align=\"left\"\u003e\n\u003cp\u003evisitor\u003c/p\u003e\n\u003c/th\u003e\n\u003c/tr\u003e\n\u003c/thead\u003e\n\u003ctbody\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003eadd equipment to workflow steps\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003edefine usage and cost\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ecreate new group\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003eadd members\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003enominate administrators within the group\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003eadministrate authorization (user/visitor)\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ecreate a project within a group\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003eassign user to a project\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ecreate an experiment within a project\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003eInform the path to the working folder and generate the storage architecture\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003eadd data to an experiment\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003eread an experiment\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003eprint and experiment report\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003esee and print invoice\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\n\u003cp\u003ex\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n\u003c/tr\u003e\n\u003c/tbody\u003e\n\u003c/table\u003e\n\u003c/div\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec5\" class=\"Section2\"\u003e\n\u003ch2\u003eEquipment Setup in F\u0026deg;Low:\u003c/h2\u003e\n\u003cp\u003eIn F\u0026deg;Low, the facility manager possesses exclusive access to a designated page termed \"parameters\", facilitating the seamless association of equipment with predefined workflow steps essential for sample preparation in electron microscopy (EM) projects. These steps encompass a comprehensive range of processes from sample immobilization to final imaging, ensuring coverage of the most common sample preparation procedures encountered in biological research. The predefined steps within F\u0026deg;Low include:\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003eSample Immobilization: Chemical fixation, Plunge freezing, High-pressure freezing\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eCryo Light Microscopy\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eDehydration \u0026ndash; Embedding / Freeze-substitution\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eIn-Resin Fluorescence\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eUltramicrotomy \u0026ndash; Thinning\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eOn-section Light Microscopy\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eElectron Microscopy\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eCLEM Registration (Correlative Light and Electron Microscopy)\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eOther\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eThe inclusion of these steps reflects a comprehensive approach to sample preparation, spanning from live specimen handling to advanced EM imaging techniques. The facility manager is empowered to populate each step with relevant equipment or products, tailoring the setup to the specific requirements and resources of the facility. Furthermore, the manager can assign a cost per unit, room, session, or hour to each equipment entry, thereby facilitating accurate cost estimation for experiments conducted within the facility.\u003c/p\u003e\n\u003cp\u003eThese cost estimates play a pivotal role in determining the overall expense associated with a particular experiment, enabling the generation of invoices in alignment with the facility's internal charging policy. The granularity of cost breakdown is customizable within each facility, reflecting its unique operational structure and financial considerations.\u003c/p\u003e\n\u003cp\u003eBy integrating equipment setup and cost estimation functionalities within F\u0026deg;Low, the platform streamlines project management, enhances financial transparency, and ensures efficient resource allocation within electron microscopy facilities. This integrated approach fosters accountability and optimization, ultimately facilitating the execution of high-quality research endeavors.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec6\" class=\"Section2\"\u003e\n\u003ch2\u003eCreating Projects and Associated Experiments in F\u0026deg;Low:\u003c/h2\u003e\n\u003cp\u003eUpon accessing the group leader page, users are presented with their entitled projects, as determined by affiliations established by the group leader or administrators. Each project within F\u0026deg;Low is a structured collection of experiment sets, facilitating organized management and tracking of research endeavors.\u003c/p\u003e\n\u003cp\u003eTo initiate an experiment within a project, the user begins by assigning a name to the experiment and specifying a starting date. Subsequently, the user proceeds to create the experiment structure, which involves subdividing it into several sequential steps, each necessitating a specific set of apparatus for execution.\u003c/p\u003e\n\u003cp\u003ePlanning experiments within F\u0026deg;Low entails selecting a step from the experiment structure and associating the appropriate equipment, along with entering expected volume and date of use (optional). Acknowledging the potential variance between anticipated and actual time investments, users have the flexibility to update the actual volume expended, enabling recalibration of the final cost estimation for the experiment.\u003c/p\u003e\n\u003cp\u003eIntegral to this process is the specification of the \"work folder path\" where future experiment data will be stored. This feature ensures long-term sample traceability, even years after project initiation, mitigating the risk of data loss and facilitating data retrieval for subsequent analyses or reference.\u003c/p\u003e\n\u003cp\u003eAdditionally, users are encouraged to provide contextual \u0026ldquo;comments\u0026rdquo; on the project, enhancing understanding of the experiment's objectives and significance.\u003c/p\u003e\n\u003cp\u003eUpon completion or update, users have the option to populate the experiment with relevant data sections or navigate to it if the experiment already exists within the system. This streamlined workflow in F\u0026deg;Low empowers researchers to efficiently manage and execute their experiments while promoting data integrity and accessibility throughout the project lifecycle.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec7\" class=\"Section2\"\u003e\n\u003ch2\u003eExperiment Management in F\u0026deg;Low:\u003c/h2\u003e\n\u003cp\u003eThe experiment page within F\u0026deg;Low comprises three main areas designed to streamline experiment organization and execution, ensuring comprehensive tracking and documentation of sample transformations:\u003c/p\u003e\n\u003cp\u003e1. Navigation Panel:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eLocated at the top row, this panel enables quick navigation between the group leader, project, and individual experiments, facilitating seamless access to pertinent information.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003e2. Experiment Structure:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eThe left column is divided into two sections:\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eThe top section presents the predefined steps established during experiment creation, logically ordered from live sample handling to correlative light and electron microscopy (CLEM), enabling a chronological overview of sample processing.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eThe bottom section lists the samples contained within the specific experiment, allowing for comparative analysis of sample evolution across different steps.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003e3. Central Information Panel:\u003c/p\u003e\n\u003cp\u003eThe central section of the experiment page provides detailed information on the consulted step, offering insights into key procedures and considerations:\u003c/p\u003e\n\u003cp\u003eA. Sample Fixation/Vitrification:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eProvides a comprehensive overview of the fixation/vitrification process, including pre-fixation conditions and the vitrification method if conducted during the experiment.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eAllows insertion of images captured before immobilization (Heiligenstein et al., 2021; Koning et al., 2014, 2022) and diagrams illustrating the high-pressure freezing (HPF) protocol.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eOffers a spacious commentary area to document diverse fixation approaches, sample characteristics, and preparation details.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eB. Cryo Light Microscopy:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eAllows inclusion of representative images to depict this step, aiding in visualizing experimental outcomes.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eProvides space for user comments and annotations for enhanced documentation.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eC. Freeze-Substitution/Staining/Dehydration/Embedding:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eAcknowledges the complexity and duration of the freeze-substitution process, often involving multiple samples across various experiments (supplementary Fig.\u0026nbsp;1).\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eFacilitates creation and application of freeze-substitution (FS) protocols to multiple independent experiments, streamlining workflow efficiency.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eSupports both conventional chemical fixation and FS procedures, accommodating diverse experimental protocols and approaches.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eEach step can be detailed precisely in temperature, temperature ramp, time, reagents and solvents. This table form may be imported or exported in a CSV format. Template may therefore be used to speed-up the completion time and adjusted to each batch if necessary.\u003c/p\u003e\n\u003cp\u003eD. In-Resin Fluorescence Microscopy:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eOffers provision for inclusion of representative images for visual illustration.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eEncourages user input through comments and annotations to enrich experiment documentation.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eHere, the acquisition metadata are inserted in the manufacturer proprietary format for later reuse.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eE. Ultramicrotomy:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eEnsures compliance with FAIR principles by enabling storage box linkage for EM grids post-experiment.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eFacilitates efficient organization and labelling of storage boxes, enhancing long-term sample traceability.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eSupports Tokuyasu immunolabeling assignment to individual EM grids, enabling precise tracking of labelling trials.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eThe box table may be printed to be completed at the bench.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eF. On-Section Microscopy:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eProvides space for representative images and user comments, enhancing documentation clarity and completeness. Comparable to Cryo Light Microscopy, In Resin Microscopy. This section applies particularly to \u0026lsquo;on section fluorescence microscopy\u0026rsquo; or \u0026lsquo;array tomography\u0026rsquo; approaches.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eG. Electron Microscopy:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eAllows inclusion of representative images and user comments for comprehensive experiment documentation.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eH. CLEM Registration:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eFacilitates illustration of the CLEM workflow through representative images from light microscopy, electron microscopy, and CLEM stages.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eOffers space for user comments to capture additional insights and observations.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eThis centralized information panel serves as a comprehensive repository for documenting experiment details, ensuring clarity, reproducibility, and adherence to FAIR principles in electron microscopy research.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec8\" class=\"Section2\"\u003e\n\u003ch2\u003eData Organization:\u003c/h2\u003e\n\u003cp\u003eF\u0026deg;Low promotes adherence to FAIR principles by recommending a predetermined folder architecture within the experiment folder, ensuring long-term findability of experiment data. This architecture includes folders for live data, curve data, block data, SEM images, TEM images, and image analysis results, or a similar structure validated by the working environment.\u003c/p\u003e\n\u003cp\u003eIt embraces a broad perspective, that may target the user to more dedicated metadata generated by each apparatus used in the protocol.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec9\" class=\"Section2\"\u003e\n\u003ch2\u003eExperiment Report Sharing:\u003c/h2\u003e\n\u003cp\u003eTo facilitate experiment exploration and report transmission, F\u0026deg;Low enables the printing of a concise 2-page PDF summary of the experiment (supplementary file 1). This summary can be stored at the root of the sample and shared with collaborators or stakeholders.\u003c/p\u003e\n\u003cp\u003eInternally, physical samples are affixed to printed PDF summaries, creating accurate time stamps for each sample and eliminating untraceable sample blocks.\u003c/p\u003e\n\u003cp\u003eBy integrating these features, F\u0026deg;Low enhances experiment management, documentation, and sharing, promoting transparency, reproducibility, and efficiency in electron microscopy research endeavors.\u003c/p\u003e\n\u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eElectron microscopy (EM) remains a cornerstone technique in biological research, offering unparalleled resolution and insight into cellular structures and dynamics. However, despite its established utility, the adoption of EM is hindered by several challenges, perpetuating a perception of high expertise requirements and hindering widespread utilization.\u003c/p\u003e\n\u003cp\u003eSeveral publications point out to the data management, in the perspective of the large volume generated (Poger et al., 2023; Rzepka et al., 2023). We acknowledge this challenge, but focus more on the detailed transformation of the sample, undertaking variable but predictable pathways.\u003c/p\u003e\n\u003cp\u003eOne significant challenge lies in the lack of standardized protocols for sample preparation, leading to a fragmented and artisanal approach to EM. The absence of streamlined protocols makes it daunting for scientists to navigate the intricate pathways from live samples to EM imaging. As a result, accessing precise protocols often entails contacting authors directly or relying on non-standardized documentation, impeding efficient knowledge transfer within and across research laboratories.\u003c/p\u003e\n\u003cp\u003eExploring existing solutions in the field, we identified several software offerings aiming to address aspects of EM workflow management. ThermoFisherScientific\u0026apos;s Athena Software and PPMS from Stratocore focus primarily on image analysis and resource management, respectively, but lack comprehensive support for project management and sample tracking from an individual user perspective. Similarly, the EMPIAR database\u0026apos;s Sample Preparation Widget aims to synthesize complex workflows but falls short in tracking individual samples and facilitating routine experiment management.\u003c/p\u003e\n\u003cp\u003eIn contrast, our solution, F\u0026deg;Low, emphasizes the standardization and tracking of individual experiments, aligning closely with the FAIR principles (Findable, Accessible, Interoperable, and Reusable). By providing a user-friendly interface for creating and managing experiments, F\u0026deg;Low streamlines the sample preparation process and enhances knowledge transmission within research teams. Unlike existing solutions, F\u0026deg;Low prioritizes the identification of appropriate samples and the iterative improvement of protocols through a systematic and synthetic overview from the outset of the experiment.\u003c/p\u003e\n\u003cp\u003eIn conclusion, while existing Data Management software solutions offer valuable contributions to resource management and reporting, F\u0026deg;Low distinguishes itself by focusing on individual experiment tracking and protocol refinement. By standardizing the tracking process and promoting adherence to FAIR principles, F\u0026deg;Low represents a significant step towards democratizing EM and fostering efficient knowledge transmission in biological research.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n \u003cli\u003eHeiligenstein, X., de Beer, M., Heiligenstein, J., Eyraud, F., Manet, L., Schmitt, F., Lamers, E., Lindenau, J., Kea-te Lindert, M., Salamero, J., Raposo, G., Sommerdijk, N., Belle, M., \u0026amp; Akiva, A. (2021). \u003cem\u003eHPM live \u0026mu; for a full CLEM workflow\u003c/em\u003e (pp. 115\u0026ndash;149). https://doi.org/10.1016/bs.mcb.2020.10.022\u003c/li\u003e\n \u003cli\u003eKoning, R. I., Faas, F. G., Boonekamp, M., de Visser, B., Janse, J., Wiegant, J. C., de Breij, A., Willemse, J., Nibbering, P. H., Tanke, H. J., \u0026amp; Koster, A. J. (2014). MAVIS: an integrated system for live microscopy and vitrification. \u003cem\u003eUltramicroscopy\u003c/em\u003e, \u003cem\u003e143\u003c/em\u003e, 67\u0026ndash;76. https://doi.org/10.1016/j.ultramic.2013.10.007\u003c/li\u003e\n \u003cli\u003eKoning, R. I., Vader, H., van Nugteren, M., Grocutt, P. A., Yang, W., Renault, L. L. R., Koster, A. J., Kamp, A. C. F., \u0026amp; Schwertner, M. (2022). Automated vitrification of cryo-EM samples with controllable sample thickness using suction and real-time optical inspection.\u0026nbsp;\u003cem\u003eNature Communications 2022 13:1\u003c/em\u003e, \u003cem\u003e13\u003c/em\u003e(1), 1\u0026ndash;10. https://doi.org/10.1038/s41467-022-30562-7\u003c/li\u003e\n \u003cli\u003ePoger, D., Yen, L., \u0026amp; Braet, F. (2023).\u0026nbsp;\u003cem\u003eBig data in contemporary electron microscopy: challenges and opportunities in data transfer, compute and management\u003c/em\u003e. \u003cem\u003e160\u003c/em\u003e, 169\u0026ndash;192. https://doi.org/10.1007/s00418-023-02191-8\u003c/li\u003e\n \u003cli\u003eRzepka, N., Bogovic, J. A., \u0026amp; Moore, J. A. (2023). Toward scalable reuse of vEM data: OME-Zarr to the rescue. \u003cem\u003eMethods in Cell Biology\u003c/em\u003e, \u003cem\u003e177\u003c/em\u003e, 359\u0026ndash;387. https://doi.org/10.1016/BS.MCB.2023.01.016\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-4133153/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4133153/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eElectron microscopy (EM) plays a crucial role in biological research, yet its widespread adoption is hindered by the lack of standardized protocols and efficient workflow management. This study addresses this challenge by introducing F\u0026deg;Low, a novel software solution designed to streamline the tracking and management of individual experiments in EM sample preparation. We highlight its focus on project management, sample tracking, and protocol refinement. F\u0026deg;Low prioritizes adherence to FAIR principles and facilitates knowledge transmission by providing a user-friendly interface for experiment creation and management. By standardizing the tracking process and promoting protocol improvement from the outset, F\u0026deg;Low aims to transmit EM expertise and enhance efficiency in biological research.\u003c/p\u003e","manuscriptTitle":"F°Low : EM goes FAIR. A novel database software to track with high accuracy the journey of a biological sample towards electron microscopy analysis.","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-03-21 17:38:46","doi":"10.21203/rs.3.rs-4133153/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"955cefcd-53b6-4cb6-8a33-7290bec75f28","owner":[],"postedDate":"March 21st, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":29691574,"name":"Biological sciences/Biological techniques/Software"},{"id":29691575,"name":"Scientific community and society/Scientific community/Research management"},{"id":29691576,"name":"Scientific community and society/Business and industry/Industry"},{"id":29691577,"name":"Scientific community and society/Scientific community/Research data/Databases"}],"tags":[],"updatedAt":"2024-03-25T20:35:21+00:00","versionOfRecord":[],"versionCreatedAt":"2024-03-21 17:38:46","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-4133153","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4133153","identity":"rs-4133153","version":["v1"]},"buildId":"WrCJVZZCHTDjtuVLN7oU0","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}