Promotion of the collections of the French National Museum of Natural History

The e-col+ project, led by the National Museum of Natural History, aims to showcase France’s natural history collections through digitisation. By establishing 3D digitisation workflows and developing artificial intelligence tools, the project enables researchers to utilize and enrich these resources.

NOVITOM was selected to provide outsourced microtomography services. High-resolution scans of an entomological collection were performed at the Grenoble ESRF synchrotron, using the BM05 and BM18 instruments.

What makes this project unique is the large number of specimens to be scanned, as well as their fragility.

NOVITOM has developed a specific protocol for analysing microtomographic data. Once the samples have been received, the first step involves planning and carrying out the acquisition of synchrotron microtomography data, as well as the reconstruction of that data.

A 3D U-Net architecture is trained to segment the annotated data generated using NOVITOM’s manual labelling software. A mesh is then created. To do this, the segmented data is dilated to fill in small gaps, then the dilated volume is converted into a 3D mesh, and finally the complexity of the mesh is reduced whilst retaining its overall shape. This lightweight final rendering makes it easy to share the results obtained.

The data analysis protocol was presented at the Technart2025 international conference, which took place in Perugia (Italy).

Le projet « e-COL+ Valorisation des données naturalistes » is supported by a grant from the French government managed by the ‘ANR, the French National Research Agency  (ANR-21-ESRE-0053 PIA3)

As an independent laboratory, Novitom enables organisations of all kinds to access synchrotron micro- and nano-tomography.

  • Regular access to synchrotron facilities’ instruments
  • Expertise in experimental design for high-resolution phase-contrast microtomography
  • Expertise in extracting information and physical parameters from 3D images, in combination with auxiliary techniques

 

>>Our services and expertise in natural and cultural heritage

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