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Welcome to the 3D Leaf Atlas (beta). This interactive platform will provide researchers, students, educators, and the general public an opportunity to visually explore the stunningly complex and diverse geometries that leaves have evolved during the last 400+ million years.

The 3D leaf segment that you see here began as an X-ray microcomputed tomography (microCT) image collected at Lawrence Berkeley National Laboratory's Advanced Light Source (ALS), beamline 8.3.2. Different materials absorb more and less X-ray energy. So, depending on a leaf's internal structure, such as the relative volume of cell versus air, different amounts of X-ray are transmitted through the leaf to the sensor. In this scan, the veins and non-leaf regions have been removed and show up as white. The relative X-ray absorption goes from low (black) to high (grey/white). Thus, cells which absorb more X-ray than air show up as grey and black, respectively. See the User Interface section below for help using the panels to the right.

X-Ray MicroCT Image

Species: Hechtia caerulea
Family: Bromeliaceae
Size: 323 x 426 x 95 um3
Color Depth: 8 bits
Image size: 12 MB
Download Raw MicroCT
Download Labeled MicroCT
Download 3D Mesh

Image Classification
Image Classification

Based on the spatial distribution X-ray absorption, we can then classify the different material present in leaf (try clicking the 'label map' box twice). In this example, black is background, dark grey is vein, light grey is cell, and white is intercellular airspace. Or try adding a 3D mesh of the intercellular airspace by clicking 'visible' under the mesh folder.

User Interface
User Interface

Check out the User Interface panel on the right side of the screen. Use your mouse to orbit (click-and-hold left button), pan (click-and-hold wheel), and zoom (scroll wheel). You can move through different slices of the 3D scan by using the 'IndexX', 'IndexY', and 'IndexZ' sliders. Try changing the 'lowerThreshold' and 'upperThreshold ' sliders to see if you can get a better view of the cell or intercellular airspace 3D geometry.