The Data Sets - Olfactory Projection Fibers
Folder Contents:
This is 1 of the 5 datasets used for the DIADEM Grand Challenge Qualifiers Round.
This dataset consists of 6 separate drosophila olfactory axonal projection image stacks. Manual reconstructions are provided for 3 of these 6 image stacks to be used for training (see 'General README'). Contestant traces using the other 3 image stacks will be officially scored for the Qualifiers Round.
Experimental Procedures:
Dataset owner: GSXE Jefferis, Department of Zoology, University of Cambridge
Species: Drosophila
Strain: y w hs-FLP UAS-mCD8-GFP/+ or Y; FRTG13 tubP-GAL80/FRTG13 GAL4-GH146 UAS-mCD8-GFP
Nervous System Region: Olfactory Bulb
Fiber type: Axons
Labeling Method: GFP
Image Acquisition Method: 2-channel confocal microscopy
Tracing Method: Neurolucida (Colchester, VT)
Objective Lens: 40x oil (NA=1.3) with 1.5x zoom
See Jefferis GS et al., 2007, Cell Vol 128(6) for general information related to the data
Z distance between successive images within an image stack: 3.03 pixels
Download Instructions:
1. Download and extract 'Olfactory Projection Fibers v2.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 3 subfolders,
'OP_1' through 'OP_3'.
5. 'Qualifier Image Stack' folder will contain 3 subfolders,
'OP_4' through 'OP_6'.
6. 'Manual Reconstructions' folder will contain 3 files:
'OP_1.swc' through 'OP_3.swc' where number corresponds to
the image stack number to which they belong.
7. Each SWC file is a manually-traced digital reconstruction
traced in 3 dimensions (X,Y, and Z).
8. SWC files will align properly with image stacks when loaded
into software that uses pixel-based coordinates, such as ImageJ
or Neuromantic.
9. Each image stack contains only 1 axonal projection to be
traced.
10. Image stacks may contain other overlapping projections that
should not be traced.
11. Starting coordinates are given below that mark the root of
the correct projection to reconstruct.
12. Special note for this dataset: External branches (i.e. branches that end in a termination) with path lengths of less than 6 pixels will be ignored in the scoring process. Thus, they can be traced or ignored by the contestant without affecting the score, provided that the traced branches remain less than 6 pixels in length.
Manual reconstruction OP_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 512x512 pixels in XY):
OP_1- Number of images: 60
OP_2- Number of images: 88
OP_3- Number of images: 62
OP_4- Number of images: 67
OP_5- Number of images: 76
OP_6- Number of images: 101
Manual Reconstruction Starting Coordinates (X and Y in pixels; Z in image sequence number, where top image Z = 0):
OP_1 (X,Y,Z): (30.979,429.04,0.000); Training tree; Manual reconstruction provided
OP_2 (X,Y,Z): (0.72501,391.08,25); Training tree; Manual reconstruction provided
OP_3 (X,Y,Z): (93.742,179,38); Training tree; Manual reconstruction provided
OP_4 (X,Y,Z): (128.2,504.37,0.303); Scored tree; Manual reconstruction not provided
OP_5 (X,Y,Z): (185.7,264.02,33); Scored tree; Manual reconstruction not provided
OP_6 (X,Y,Z): (15.074,412.01,10); Scored tree; Manual reconstruction not provided