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EMC-SCA: Electron Microscopy Center - Scalable Compute Archive

In June, 2014, a group headed by Arvind Gopu from the Pervasive Technology Institute (PTI) at IU Bloomington released version 1.0 of what is now called the EMC-SCA (Electron Microscopy Center - Scalable Compute Archive). This is our web portal for browsing images recorded using the JEOL JEM 3200FS and other instruments in the EMC. Members of the IUB and IUPUI communities can login through the CAS login system using their campus-wide username and passphrase and outside users can create their own accounts (user names and passwords).

At present, the EMC-SCA is a tag searchable image browser and explorer. It will eventually contain the entire set of images recorded using the 3200FS and the JEOL JEM 1400plus. Searches are based on tags associated with the images during or after the upload process and/or on microscope acquisition parameters stored in their DigitalMicrograph metadata. We are also slowly adding to the "compute" (formerly the "pipeline") aspect of the portal (i.e., the ability to spawn various image processing jobs to the IUB computer clusters). We have implemented some file format conversion (including size reduction) and plan to add defocus estimation for cryoEM images. We may attempt to do particle selection via the pipeline, but that is a more ambitious task and may not ever happen. Users can build various collections of images using the portal, then manage and download the collections (or individual imatges) to any internet-accessible location.

At present, dm3 or dm4 files from any microscope (including the JEOL JEM 1010) can be added to the portal. This allows users to archive images recorded at other locations. The best way to include such images in the portal is to contact David Morgan.

If this portal is useful, we will expand it to include non-DigitalMicrograph images recorded using the 3200FS (e.g., images acquired using the Oxford EDX software) and images from the FEI Teneo Volume Scope. Please contact David Morgan for further information about the portal.