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Zebra Finch Syrinx Anatomy

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Digital three-dimensional maps of male and female zebra finch syrinx. Detailed descriptions of these maps can be found in an accompanying paper. Please cite the article as:

Düring DN, Ziegler A, Thompson CK, Ziegler A, Faber C, Müller M, Scharff C, Elemans CPH (2013) The songbird syrinx morphome: a three-dimensional, high-resolution, interactive morphological map of the zebra finch vocal organ. BMC Biology 2013 11:1. doi:10.1186/1741-7007-11-1

 

3D PDF Models

We have prepared interactive 3D PDF files that can be viewed with Adobe Acrobat Reader version 9 or higher (http://www.adobe.com). Click on the figure to activate the 3D features. Note that 3D features are not supported in Preview for Mac.

ZF Male 3D Syrinx Morphome (3D PDF, 7.3 Mb)

To keep the PDF size of the morphome manageable, the size of the models is drastically reduced. Therefore, very thin parts such as muscle insertions and the ends of muscles do not always appear to be correctly placed. Please refer to text and figures of the accompanying paper for exact descriptions.

Raw Data

The raw µCT data is available for community use and further annotation. Each µCT scan can be downloaded as a single ZIP archive that contains a stack of images (voxel intensity data). These stacks require >4 Gb of memory. In addition an accompanying annotation file ('.am' extension) contains the labels of the different structures. These latter files are much smaller and can be loaded on systems with less memory.

Uncontrasted µCT scan (bone only)

ZF Male Syrinx TIFF-stack (ZIP archive, 136 Mb)

ZF Male Syrinx AM-labels (Amira label file, 7 Mb)

 

Instructions to view µCT data with Amira (http://www.amira.com/)

1)   Download the above ZIP archive and unzip.

2)   Open Amira

3)   Load the TIFF-stack into Amira (>open>) and try to use the option "Read complete volume into memory". The "Image Read Parameter"-Box will open, enter scale: x=10, y=10, z=10 to get measures in micrometers. A module will appear in the left panel.

4)   Right-click the module and select "View>Isosurface". Set the threshold to about 0.36 and click Apply.

Instructions to view only bone isosurface with Amira

1)   Open Amira

2)   Load the file 'ZF_male_syrinx_uncontrastscan_AMLabels.am' which contains the isosurface as a labelfield. A module appears in the left window.

3)   Right-click the module, select "SurfaceGen", and press 'Apply'. This will generate the surface and may take some time.

10)  A new module ".surf" will appear in the left panel. Right-click this module and select "Surfaceview" which will render the surface on the screen.

 

The data can also be viewed with the free software ImageJ (http://rsbweb.nih.gov/ij/)

 

Iodine (IKI) contrasted µCT scan (all tissues)

ZF Male Syrinx IKI TIFF-stack (ZIP archive, 181 Mb)

ZF Male Syrinx IKI AM-labels (Amira label file, 9 Mb)

Instructions to view µCT and morphome data with Amira (http://www.amira.com/)

1)   Download one of the ZIP archives and unzip.

2)   Open Amira

3)   Load the TIFF-stack into Amira (>open>) and try to use the option "Read complete volume into memory". The "Image Read Parameter"-Box will open, enter scale: x=10, y=10, z=10 to get measures in micrometers. A module will appear in the left panel (module A).

4)   Load the "Male_ZF_morphome.am"-file (>open>) with annotation data. An additional module will appear (module B).

5)   Left-click the white box in module B and select "ImageData".

6)   Connect it to module A.

7)   Select module B and click on the "Image Segmentation Editor"-icon in the bottom box to view the labeled scan data.

8)   To view only the scan data, select module A, right-click and choose OrthoSlice.

9)   To view the data in 3D surfaces, click module B, select "SurfaceGen", and press 'Apply'. This will generate surfaces and may take some time.

10)  A new module ".surf" will appear in the left panel (Module C). Right-click the module and select "surfaceview" which will render the surfaces on the screen.

 

The data can also be viewed with the free software ImageJ (http://rsbweb.nih.gov/ij/) using the Amira Plugin.

 

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