The Data Sets - Cerebellar Climbing Fibers
Folder Contents:
This is 1 of the 5 datasets used for the DIADEM Grand Challenge Qualifiers Round.
This dataset consists of 2 separate cerebellar climbing fiber image stacks. A manual reconstruction is provided for 1 of these 2 image stacks to be used for training (see 'General README'). Contestant reconstructions using the other image stack will be officially scored for the Qualifiers Round.
Experimental Procedures:
Dataset owners: GA Ascoli, Molecular Neuroscience Department, Krasnow Institute for Advanced Study, George Mason University (Imaging and Reconstructions); I Sugihara, Department of Systems Neurophysiology, Tokyo Medial 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 (Colchester, 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 'Manual
Reconstructions'.
3. 'Image Stacks' folder will contain 2 subfolders: 'Training
Image Stack' and 'Qualifier Image Stack'.
4. 'Training Image Stack' folder will contain 1 subfolder: 'Image
Stack CF_1'.
5. 'Qualifier Image Stack' folder will contain 1 subfolder:
'Image Stack CF_2'.
6. 'Manual Reconstructions' folder will contain 1 subfolder:
'Manual Reconstruction CF_1' which corresponds to 'Image Stack
CF_1'.
7. 'Manual Reconstruction CF_1' contains a manually-traced
digital reconstruction ('CF_1.swc') that was traced in 3
dimensions (X,Y, and Z) using 'Image Stack CF_1'.
8. 'CF_1.swc' will align properly with 'Image Stack CF_1' 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.
Manual 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:
CF_1- Number of images: 34; Resolution: 6120 x 4343
CF_2- Number of images: 28; Resolution: 5100 x 3102
Manual 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); Training tree; Manual reconstruction provided
CF_2 (X,Y,Z): (818,332,6); Scored tree; Manual reconstruction not provided