Sample Preparation Widget (SPW)

The Sample Preparation Widget (SPW) is an online tool available through the EMPIAR deposition system. SPW is an easy-to-use and re-usable web component that allows for the detailed and structured description of Sample Preparation (SP) protocols used for volume EM (vEM) experiments. The widget (working with a Mongo database) provides a repository of SP data that can be shared with other users and used for further analysis.
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The SPW was designed in collaboration with Kedar Narayan, Michele Darrow and Carles Bosch Pinol of the Sample Preparation Working Group which is a part of the volume EM community initiative. It allows for easy to use point-and-click functionality, using controlled vocabularies where possible and allowing free-text information only if absolutely required. The tool was primarily designed to produce protocols that can accompany vEM datasets deposited to EMPIAR, but it can also be used to upload, view, edit, copy, and download entries for use at the bench.
If you use the Sample preparation widget, please cite: Sriram Somasundaram, Carles Bosch, Michele C. Darrow, Gerard J. Kleywegt, Ardan Patwardan and Kedar Narayan (2022). “The Sample Preparation Widget: a new tool in EMPIAR to create structured sample-preparation protocols for volume electron microscopy ”, to be published.

How to use SPW

  • Users will need to register with the EMPIAR deposition system to access the widget.
  • Once a newly registered user has been authenticated, they will be directed to the home page of the widget.
  • The home page contains a simple help section, which provides new users with definitions and a basic set of guidelines for use of the main widget controls. Once the user decides to create a protocol, they are given the option to start building a protocol from scratch or to edit a previously loaded protocol, either one that is available publicly or one previously created by the same user.
  • Workflows in SPW have two different accessibility scopes: private and public. Users can create as many workflows as they want using the widget in the private scope.
  • Once a workflow is submitted users will be able to publish the SP data. Saved protocols can be accessed within SPW in read-only mode. The protocols can be downloaded in JSON format and as images in PNG and SVG format (e.g., to include in reports or notebooks or as part of a manuscript submission).


The work on EMPIAR was funded from 2014 to 2021 by two project grants awarded to EMBL-EBI by MRC and BBSRC [MR/L007835/1, MR/P019544/1]. Since 2021, it benefits from funding from the Wellcome Trust [221371/Z/20/Z]. The work on SPW and EMPIAR is further supported by EMBL with funding from its member states.