{"id":13349,"date":"2026-10-15T09:40:42","date_gmt":"2026-10-15T09:40:42","guid":{"rendered":"https:\/\/www.embl.org\/about\/info\/imagine\/?p=13349"},"modified":"2026-10-15T09:51:58","modified_gmt":"2026-10-15T09:51:58","slug":"seeing-inside-a-marine-sponge-in-3d-and-without-a-single-cut","status":"publish","type":"post","link":"https:\/\/www.embl.org\/about\/info\/imagine\/blog\/2026\/10\/seeing-inside-a-marine-sponge-in-3d-and-without-a-single-cut\/","title":{"rendered":"Seeing inside a marine sponge, in 3D and without a single cut"},"content":{"rendered":"\n

How a Greek marine research centre is helping test X-ray imaging for climate-related marine research<\/strong><\/em><\/h1>\n\n\n\n

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This article is written <\/em>by<\/p>\n\n<\/div>\n<\/div>\n\n\n

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\n Niki Keklikoglou<\/a>\n <\/h3>\n \n

\n HCMR <\/p>\n \n \n \n\n \n<\/article>\n\n<\/div>\n<\/div>\n\n\n

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\n Kamila Sfugier Tollik <\/a>\n <\/h3>\n \n

\n EMBRC <\/p>\n

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and co-written by<\/em><\/p>\n\n<\/div>\n<\/div>\n\n\n

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\n Ksenia Denisova<\/a>\n <\/h3>\n \n

\n EMBL Hamburg <\/p>\n

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Marine organisms are at the front line of climate change, but studying how they respond often means cutting, staining or drying precious samples. Within IMAGINE, the Hellenic Centre for Marine Research (HCMR) is helping to show that there is a better way.<\/p>\n\n\n\n

HCMR is a partner in Work Package 9 (WP9), led by EMBRC-ERIC, which tests whether the imaging technologies developed in IMAGINE are ready to serve marine researchers. HCMR’s first test case, with the X-ray imaging technology of WP1, is a sponge.<\/p>\n\n\n\n

The power of testing together<\/strong><\/h2>\n\n\n\n

HCMR brings marine biology expertise and real research questions. EMBL Hamburg and the IMAGINE X-ray team bring cutting-edge imaging. EMBRC-ERIC connects the two, so that new technologies are shaped by the needs of marine researchers from the start.<\/p>\n\n\n\n

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3D volume rendering of the marine sponge Chondrilla nucula, acquired with phase-contrast high-throughput X-ray tomography (HiTT). The star-shaped structures are sclerites, the sponge’s tiny skeletal elements. Credit: EMBL Hamburg<\/em>.<\/figcaption><\/figure>\n\n\n\n

The research question<\/strong><\/h2>\n\n\n\n

Sponges and other benthic invertebrates that live attached to the seabed cannot move away when conditions around them change, making them particularly vulnerable to environmental pressures. HCMR studies how climate change, including ocean acidification and rising temperature, affects the form and structure of these animals. Within the framework of the national MACCIMO project, one of the species in focus is the sponge Chondrilla nucula<\/em>, sampled from different populations and from experimental treatments simulating future ocean conditions.<\/p>\n\n\n\n

The challenge<\/strong><\/h2>\n\n\n\n

HCMR had already scanned these sponges with a conventional micro-CT (SkyScan 1172). The images gave a good overview, but the resolution was too low to show fine internal structures such as sclerites, the microscopic skeletal elements. The samples also needed extra preparation: they were dried with hexamethyldisilazane (HMDS) to improve tissue contrast. This is where IMAGINE’s new X-ray technology comes in.<\/p>\n\n\n\n

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Cross-section images of Chondrilla nucula specimens obtained with SkyScan 1172 micro-CT. Credit: HCMR<\/em><\/figcaption><\/figure>\n\n\n\n

The IMAGINE solution<\/h2>\n\n\n\n

26 specimens were sent to EMBL Hamburg for phase-contrast high-throughput X-ray tomography (HiTT) at the EMBL P14 beamline on the PETRA III synchrotron at DESY. This technology can reach cellular-level resolution, using a voxel size of  660nm\u00b3 at high acquisition speeds. The samples were fixed in 4% formalin, dehydrated and stored in 70% ethanol. Because HiTT has a field of view of ~1mm x ~1mm works on each specimen was trimmed into two pieces of about 1 mm\u00b3, one from the exterior and one from the interior of the sponge, so both regions could be compared.<\/p>\n\n\n\n

Ksenia Denisova (EMBL Hamburg) collected and analysed the HiTT data and generated the images that made it possible to investigate the sponge specimens at cellular-level resolution. Her work provided the essential imaging data for the cross-scale analysis in IMAGINE, enabling comparisons between the internal and external regions of the sponges and helping to bridge structural observations across different scales<\/p>\n\n\n\n

First results<\/strong><\/h2>\n\n\n\n