Specimens per scan & Scans per media deposit

Owned by Doug Boyer
Last updated: Dec 21, 2023
2 min read

Critical rules on number of scans and specimens per media file

Each media file should hold only ONE volumetric image or mesh for ONE specimen. These should represent the results of a single scanning event except under very specific conditions. This is an un-bendable rule on MorphoSource and you will be asked to reformat your deposits if violations to it are discovered. Breaking these rules seriously hinders MorphoSource’s ability to make data findable, accessible, reusable and otherwise corrupts its ability to serve as “preservation repository” instead of just an “archive”. Each scan gets its own media record and each mesh gets its own media record. 

  • If two or more specimens are scanned together, the scan needs to be cropped into two or more scans so each file to be uploaded only contains one specimen. In such cases reflecting CT scans, the projection series cannot currently be included because there is no meaningful way of “cropping” a projection series.
  • If two or more separate elements from the same specimen are scanned together, there are more options.  The projection series of such a scan can be uploaded. The first derivative could be the reconstructed tomograms (image stack) including all elements.  Alternativly the reconstructed tomogram can be cropped into two or more stacks so each .zip file only contains one element. These cropped stacks can each be loaded as derivatives of the same projection series, or simply as independent scans if the projections are not being deposited. However, when it comes to mesh derivatives from the reconstructed image stack, there should be one mesh per media upload. In other words, even if you choose not to crop your reconstructed image series so that there is one file per element, you will still need to load each mesh as a separate derivative of that single-specimen, multi-element scan. That means, do NOT zip collections of mesh files that are independent elements together and upload them.  The media page is unable to render more than one mesh or volume at a time.
  • Never zip multiple folders containing separate volumetric images together and load such zip files to MorphoSource. 
    • This rule applies to separate volumetric files that were generated by different scanning events. I.e., NEVER zip together and upload two folders represent two different volumetric files from two different scanning events, even if they represent different parts of the same specimen or the same view of the same specimen.
    • It is also not allowable to zip separate volumetric files when they represent different derivative-results from the same parent scan.
  • There may be limited situations where more than 1 mesh can be zipped together and uploaded to a single media record, but please contact MorphoSource administrators at morphosource@duke.edu before doing so.