Improved non-destructive 2D and 3D X-ray imaging of leaf venation
Abstract Background Leaf venation traits are important for many research fields such as systematics and evolutionary biology, plant physiology, climate change, and paleoecology. In spite of an increasing demand for vein trait data, studies are often still data-limited because the development of meth...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-01-01
|
| Series: | Plant Methods |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13007-018-0274-y |
| _version_ | 1818844887840194560 |
|---|---|
| author | Julio V. Schneider Renate Rabenstein Jens Wesenberg Karsten Wesche Georg Zizka Jörg Habersetzer |
| author_facet | Julio V. Schneider Renate Rabenstein Jens Wesenberg Karsten Wesche Georg Zizka Jörg Habersetzer |
| author_sort | Julio V. Schneider |
| collection | DOAJ |
| description | Abstract Background Leaf venation traits are important for many research fields such as systematics and evolutionary biology, plant physiology, climate change, and paleoecology. In spite of an increasing demand for vein trait data, studies are often still data-limited because the development of methods that allow rapid generation of large sets of vein data has lagged behind. Recently, non-destructive X-ray technology has proven useful as an alternative to traditional slow and destructive chemical-based methods. Non-destructive techniques more readily allow the use of herbarium specimens, which provide an invaluable but underexploited resource of vein data and related environmental information. The utility of 2D X-ray technology and microfocus X-ray computed tomography, however, has been compromised by insufficient image resolution. Here, we advanced X-ray technology by increasing image resolution and throughput without the application of contrast agents. Results For 2D contact microradiography, we developed a method which allowed us to achieve image resolutions of up to 7 µm, i.e. a 3.6-fold increase compared to the industrial standard (25 µm resolution). Vein tracing was further optimized with our image processing standards that were specifically adjusted for different types of leaf structure and the needs of higher imaging throughput. Based on a test dataset, in 91% of the samples the 7 µm approach led to a significant improvement in estimations of minor vein density compared to the industrial standard. Using microfocus X-ray computed tomography, very high-resolution images were obtained from a virtual 3D–2D transformation process, which was superior to that of 3D images. Conclusions Our 2D X-ray method with a significantly improved resolution advances rapid non-destructive bulk scanning at a quality that in many cases is sufficient to determine key venation traits. Together with our high-resolution microfocus X-ray computed tomography method, both non-destructive approaches will help in vein trait data mining from museum collections, which provide an underexploited resource of historical and recent data on environmental and evolutionary change. In spite of the significant increase in effective image resolution, a combination of high-throughput and full visibility of the vein network (including the smallest veins and their connectivity) remains challenging, however. |
| first_indexed | 2024-12-19T05:20:55Z |
| format | Article |
| id | doaj.art-60d8b459ac1e4f5d80358037e5a3bf26 |
| institution | Directory Open Access Journal |
| issn | 1746-4811 |
| language | English |
| last_indexed | 2024-12-19T05:20:55Z |
| publishDate | 2018-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Plant Methods |
| spelling | doaj.art-60d8b459ac1e4f5d80358037e5a3bf262022-12-21T20:34:30ZengBMCPlant Methods1746-48112018-01-0114111510.1186/s13007-018-0274-yImproved non-destructive 2D and 3D X-ray imaging of leaf venationJulio V. Schneider0Renate Rabenstein1Jens Wesenberg2Karsten Wesche3Georg Zizka4Jörg Habersetzer5Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum FrankfurtDepartment of Messel Research and Mammalogy, Senckenberg Research Institute and Natural History Museum FrankfurtDepartment of Botany, Senckenberg Museum of Natural History GörlitzDepartment of Botany, Senckenberg Museum of Natural History GörlitzDepartment of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum FrankfurtDepartment of Messel Research and Mammalogy, Senckenberg Research Institute and Natural History Museum FrankfurtAbstract Background Leaf venation traits are important for many research fields such as systematics and evolutionary biology, plant physiology, climate change, and paleoecology. In spite of an increasing demand for vein trait data, studies are often still data-limited because the development of methods that allow rapid generation of large sets of vein data has lagged behind. Recently, non-destructive X-ray technology has proven useful as an alternative to traditional slow and destructive chemical-based methods. Non-destructive techniques more readily allow the use of herbarium specimens, which provide an invaluable but underexploited resource of vein data and related environmental information. The utility of 2D X-ray technology and microfocus X-ray computed tomography, however, has been compromised by insufficient image resolution. Here, we advanced X-ray technology by increasing image resolution and throughput without the application of contrast agents. Results For 2D contact microradiography, we developed a method which allowed us to achieve image resolutions of up to 7 µm, i.e. a 3.6-fold increase compared to the industrial standard (25 µm resolution). Vein tracing was further optimized with our image processing standards that were specifically adjusted for different types of leaf structure and the needs of higher imaging throughput. Based on a test dataset, in 91% of the samples the 7 µm approach led to a significant improvement in estimations of minor vein density compared to the industrial standard. Using microfocus X-ray computed tomography, very high-resolution images were obtained from a virtual 3D–2D transformation process, which was superior to that of 3D images. Conclusions Our 2D X-ray method with a significantly improved resolution advances rapid non-destructive bulk scanning at a quality that in many cases is sufficient to determine key venation traits. Together with our high-resolution microfocus X-ray computed tomography method, both non-destructive approaches will help in vein trait data mining from museum collections, which provide an underexploited resource of historical and recent data on environmental and evolutionary change. In spite of the significant increase in effective image resolution, a combination of high-throughput and full visibility of the vein network (including the smallest veins and their connectivity) remains challenging, however.http://link.springer.com/article/10.1186/s13007-018-0274-yContact microradiographyImage processingLeaf clearingMicro CTVein networksVein density |
| spellingShingle | Julio V. Schneider Renate Rabenstein Jens Wesenberg Karsten Wesche Georg Zizka Jörg Habersetzer Improved non-destructive 2D and 3D X-ray imaging of leaf venation Plant Methods Contact microradiography Image processing Leaf clearing Micro CT Vein networks Vein density |
| title | Improved non-destructive 2D and 3D X-ray imaging of leaf venation |
| title_full | Improved non-destructive 2D and 3D X-ray imaging of leaf venation |
| title_fullStr | Improved non-destructive 2D and 3D X-ray imaging of leaf venation |
| title_full_unstemmed | Improved non-destructive 2D and 3D X-ray imaging of leaf venation |
| title_short | Improved non-destructive 2D and 3D X-ray imaging of leaf venation |
| title_sort | improved non destructive 2d and 3d x ray imaging of leaf venation |
| topic | Contact microradiography Image processing Leaf clearing Micro CT Vein networks Vein density |
| url | http://link.springer.com/article/10.1186/s13007-018-0274-y |
| work_keys_str_mv | AT juliovschneider improvednondestructive2dand3dxrayimagingofleafvenation AT renaterabenstein improvednondestructive2dand3dxrayimagingofleafvenation AT jenswesenberg improvednondestructive2dand3dxrayimagingofleafvenation AT karstenwesche improvednondestructive2dand3dxrayimagingofleafvenation AT georgzizka improvednondestructive2dand3dxrayimagingofleafvenation AT jorghabersetzer improvednondestructive2dand3dxrayimagingofleafvenation |