The Data Sets - Cerebellar Climbing Fibers

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Folder Contents:

This is 1 of the 6 data sets used for DIADEM.

This data set consists of 3 separate cerebellar climbing fiber image stacks, each with a corresponding gold standard reconstruction.

During the DIADEM 2010 Grand Challenge Competition: 'CF_1' was used for the Training Round, 'CF_2' for the Qualifier Round, and 'CF_3' for the Final Round.

Experimental Procedures:

Data set owners: GA Ascoli, Molecular Neuroscience Department, Krasnow Institute for Advanced Study, George Mason University (Imaging and Reconstructions); I Sugihara, Department of Systems Neurophysiology, Tokyo Medical and Dental University, Graduate School of Medicine (Histology and Labeling)

Species: Rat

Strain: Long-Evans

Nervous System Region: Cerebellar Cortex

Fiber type: Axon Terminals

Labeling Method: Biotinylated Dextran Amine (Anterograde)

Image Acquisition Method: Transmitted Light Brightfield

Tracing Method: Neurolucida (Williston, VT)

Objective Lens: 100x oil (NA=1.3) with 2.0x zoom

See Sugihara et al., 1999, J Neurol Comp Vol 414(2) for general information related to the data

Z distance between successive images within an image stack: 8.80 pixels

Download Instructions:

1. Download and extract 'Cerebellar Climbing Fibers.rar'.

2. Folder will contain 2 subfolders: 'Image Stacks' and 'Gold Standard Reconstructions'.

3. 'Image Stacks' folder will contain 3 subfolders: 'CF_1', 'CF_2', and 'CF_3'.

4. 'CF_3' will contain the subfolders 'Original' and 'Unstitched'.

5. 'Original' contains 1 image stack mosaic with image stack tiles pre-stitched similar to 'CF_1' and 'CF_2' image stacks.

6. 'Unstitched' contains the same image stack mosaic but with the tiles unstitched (see Special Notes for 'CF_3' below for details).

7. 'Gold Standard Reconstructions' contains manually traced digital reconstructions 'CF_1.swc', 'CF_2.swc', and 'CF_3.swc'. Each SWC file was traced in 3D using the image stack to which its name corresponds.

8. SWC files will align properly with their corresponding image stack when loaded into software that uses pixel-based coordinates, such as ImageJ or Neuromantic.

9. Each image stack contains only 1 axonal arbor to be traced.

10. Image stacks may contain other overlapping structures that should not be traced.

11. Starting coordinates are given below that clearly mark the root of the correct arbor to reconstruct.

Special Notes for 'CF_3':

12. Unlike other data sets where the image stack tiles were stored separately during acquisition and thus provided as unstitched (see Neocortical, Neuromuscular, and Visual Cortical data sets), the climbing fiber image stack tiles were stitched during the acquisition process. Therefore, no spatial overlap between image stacks is available. Moreover, there are some cases of subtle image stack misalignments at the borders between tiles (just like the image stack mosaics provided for 'CF_1' and 'CF_2'). For 'CF_3' only, image stack tiles were cropped from this pre-stitched image stack and saved separately in the 'Unstitched' folder. No attempts were made to improve these minor alignment offsets and the image stack translation values provided below preserve the spatial relationships of tiles in the 'Original' image stack mosaic. 1 or 2 pixels of overlap may have been artificially created for image stack tiles when unstitched in order to prevent potential gaps between tiles.

13. Image stack tile coordinates provided below for the unstitched CF_3 image stacks are for the upper left-most corner of each tile.

14. For a couple of the unstitched tiles, the stitch mark between tiles could not be found. These were arbitrarily split on the side of the given image stacks on which the stitch mark would be located.

Gold standard reconstruction 'CF_1' (light blue) is superimposed and offset (for visualization purposes) over its corresponding image stack. Arrow (red) points to the root of the reconstruction.

Individual Stack Information (All image stacks are 24 bits per pixel):

CF_1- Number of images: 34; Resolution (X,Y in pixels): (6120,4343)

CF_2- Number of images: 28; Resolution (X,Y in pixels): (5100,3102)

CF_3- Number of images: 25; Resolution (X,Y in pixels): (7000,3000)

Unstitched Image Stack Tiles Upper Left X,Y Corner Coordinates. The values below describe how far to move image stacks when they load at (X,Y,Z) = (0,0) at the upper left corner of the image stack. Note that Neuromantic (as of version 1.7.5) can load multiple and move separate image stack tiles (see Instruction 12 in 'General Readme'):

Tile X Y  
RowAColA 0 0
RowAColB 1498 0
RowAColC is not provided since it is entirely empty space in the mosaic
RowAColD 4200 0
RowAColE 5696 0
RowBColA 0 1101
RowBColB 1299 1099
RowBColC 2699 1100
RowBColD 4195 1098
RowBColE 5547 1099
RowCColA 0 2099
RowCColB 1498 2098
RowCColC 2899 2098
RowCColD 4424 2098
RowCColE 5698 2099
Dimensions (X,Y in pixels)
Tile X Y  

Gold Standard Reconstruction Starting Coordinates (X and Y in pixels; Z in image sequence number, where top image Z = 0):

CF_1 (X,Y,Z): (4882,1797,19)

CF_2 (X,Y,Z): (818,332,6)

CF_3 (X,Y,Z): (1138, 773,11)