The Data Sets - Hippocampal CA3 Interneuron
Folder Contents:
This is 1 of the 5 datasets used for the DIADEM Grand Challenge Qualifiers Round.
This dataset consists of 5 image stacks containing dendritic and axonal subtrees from one hippocampal CA3 interneuron. The material for this interneuron was sectioned into 5 slices, each of which is captured by one of the five image stacks The axonal and dendritic arbors are divided into sections and thus are broken up by section. Image stack 'Section 01' is to be used as a training set and the other 4 image stacks ('Section 02' through 'Section 05') are to be used for the scored set. All 14 'Section 01' manual reconstructions are to be used for training (see 'General README'). Contestant traces capturing the 35 other dendritic and axonal trees from 'Section 02' through 'Section 05' will be officially scored for the Qualifiers Round.
Experimental Procedures:
Dataset owner: G Barrionuevo, Department of Neuroscience, University of Pittsburgh
Species: Rat
Strain: Sprague-Dawley
Nervous System Region: Hippocampus CA3
Fiber type: Dendrites and Axons
Labeling Method: Biocytin
Image Acquisition Method: Transmitted Light Brightfield
Tracing Method: Neurolucida (Colchester, VT)
Objective Lens: 100x oil
See Calixto et al., 2008, J Physiol. Vol 586(11) for general information related to the data
Z distance between successive images within an image stack: 1.52 pixels
Download Instructions:
1. Download and extract 'Hippocampal CA3 Interneuron Part 1.rar'
through 'Hippocampal CA3 Interneuron Part 5.rar'.
2. 'Hippocampal CA3 Interneuron Part 1.rar' contains the
subfolder 'Manual Reconstructions', whereas 'Hippocampal CA3
Interneuron Part 2.rar' through 'Hippocampal CA3 Interneuron Part
5.rar' contain the subfolder 'Image Stacks'.
3. If all redundant subfolders from each RAR file are combined,
the 'Image Stacks' folder will contain two subfolders: 'Training
Image Stack' and 'Qualifier Image Stacks'.
4. 'Training Image Stack' contains image stack 'Section_01',
which is to be used with all provided training manual
reconstructions.
5. 'Qualifier Image Stacks' contains image stacks 'Section_02'
through 'Section_05' which are to be used for the 35 remaining
Qualifier Round reconstructions (see
'Manual Reconstruction Starting Coordinates'
section below for respective image stack sections).
6. All SWC files will automatically align with image stack
'Section_01' when loaded into software that uses pixel-based
coordinates, such as ImageJ or Neuromantic.
7. As is done for the training manual reconstructions provided
for this dataset, separate neuronal subtrees (e.g. trees with
starting coordinates provided below) should not be connected into
single reconstructions.
8. As is done for the both the training (provided) and qualifier
manual reconstructions (not provided), all trees are to be
reconstructed in 3D, but the Z coordinates in between bifurcation
nodes, tips, and root should be smoothed prior to submission.
That is, automated reconstructions should use linear connections
between all branch segments (i.e. between bifurcations, and
terminations, and root) for this set dataset only.
9. Image stacks may contain other overlapping structures that
should not be traced.
10. Starting coordinates are given below that clearly mark the
root of each arbor to reconstruct within its given image stack
section.
11. Special note for this dataset: External branches (i.e.
branches that end in a termination) with path lengths of less
than 23 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 23
pixels in length.
12. Special note for this dataset: A systematic method was used to decide where structures ended when they leave a given section and should be followed by contestants:
A. If a tree drifted out of focus as it left a section (i.e. lost focus near the top or bottom images), the trace is terminated at the last point in focus.
B. If a tree drifted out of focus in the middle of a section, the trace is terminated further down to where the structures is minimally visibleC. If a tree ends either continuously or abruptly but seems to reappear downstream in the same section, suggesting either a gap in labeling or that it left the section and came back, then:
i. if the gap is small enough that one can be certain that the tree continues, then the tree is traced as continuing.
ii. if the gap is too large to be certain that the branches connect, the currently traced tree is not connected to the reappearing branch.
iii. if the gap shows the branch continuing but out of focus to the point of not being able to distinguish potential arborizations, the trace is also terminated prior to the out of focus structures and not connected if it appears in focus downstream.
iv. if the gap shows the branch continuing and out of focus but visible enough to see proper connectivity, then the trace is continued through the gap, ultimately connecting the reappearing structure downstream.Ultimately, these decisions are somewhat subjective, and contestants should utilize the provided training manual reconstructions to determine the tracing style and methods used.
Manual reconstruction '01.swc' (light blue) is superimposed and offset (for visualization purposes) over image stack 'Section_01'. Arrow (red) points to the root of the reconstruction.
Individual Stack Information:
HC_1 Section_1- Number of images: 110; Pixel Size: 5360 x 3420
HC_1 Section_2- Number of images: 135; Pixel Size: 5896 x 3040
HC_1 Section_3- Number of images: 120; Pixel Size: 3752 x 2660
HC_1 Section_4- Number of images: 105; Pixel Size: 4288 x 3040
HC_1 Section_5- Number of images: 82; Pixel Size: 3752 x
2280
Manual Reconstruction Starting Coordinates (X and Y in pixels; Z in image sequence number, where top image Z = 0):
Section_01
01 (X,Y,Z): (3475,634,66); Training tree; Manual reconstruction provided
02 (X,Y,Z): (3526,667,98); Training tree; Manual reconstruction provided
03 (X,Y,Z): (3625,747,105); Training tree; Manual reconstruction provided
04 (X,Y,Z): (3926,322,37); Training tree; Manual reconstruction provided
05 (X,Y,Z): (3504,706,32); Training tree; Manual reconstruction provided
06 (X,Y,Z): (2084,1229,110); Training tree; Manual reconstruction provided
07 (X,Y,Z): (3501,703,13); Training tree; Manual reconstruction provided
08 (X,Y,Z): (3412,613,12); Training tree; Manual reconstruction provided
09 (X,Y,Z): (3333,627,16); Training tree; Manual reconstruction provided
10 (X,Y,Z): (3433,695,58); Training tree; Manual reconstruction provided
11 (X,Y,Z): (2501,1700,109); Training tree; Manual reconstruction provided
12 (X,Y,Z): (2437,1376,58); Training tree; Manual reconstruction provided
13 (X,Y,Z): (2875,983,50); Training tree; Manual reconstruction provided
14 (X,Y,Z): (3339,631,103); Training tree; Manual reconstruction provided
Section_02
01 (X,Y,Z): (4183,563,80); Scored tree; Manual reconstruction not provided
02 (X,Y,Z): (4503,1172,113); Scored tree; Manual reconstruction not provided
03 (X,Y,Z): (4063,861,108); Scored tree; Manual reconstruction not provided
04 (X,Y,Z): (3907,869,110); Scored tree; Manual reconstruction not provided
05 (X,Y,Z): (3889,839,111); Scored tree; Manual reconstruction not provided
06 (X,Y,Z): (3613,902,112); Scored tree; Manual reconstruction not provided
07 (X,Y,Z): (3357,1573,116); Scored tree; Manual reconstruction not provided
08 (X,Y,Z): (1912,2550,0); Scored tree; Manual reconstruction not provided
09 (X,Y,Z): (2466,1512,115); Scored tree; Manual reconstruction not provided
Section_03
01 (X,Y,Z): (2341,286,117); Scored tree; Manual reconstruction not provided
02 (X,Y,Z): (2094,790,101); Scored tree; Manual reconstruction not provided
03 (X,Y,Z): (1001,1336,55); Scored tree; Manual reconstruction not provided
04 (X,Y,Z): (967,1807,119); Scored tree; Manual reconstruction not provided
05 (X,Y,Z): (760,1864,57); Scored tree; Manual reconstruction not provided
06 (X,Y,Z): (770,2001,60); Scored tree; Manual reconstruction not provided
Section_04
01 (X,Y,Z): (2478,702,23); Scored tree; Manual reconstruction not provided
02 (X,Y,Z): (2487,726,84); Scored tree; Manual reconstruction not provided
03 (X,Y,Z): (3024,336,16); Scored tree; Manual reconstruction not provided
04 (X,Y,Z): (2417,823,88); Scored tree; Manual reconstruction not provided
05 (X,Y,Z): (2465,723,16); Scored tree; Manual reconstruction not provided
06 (X,Y,Z): (2443,846,19); Scored tree; Manual reconstruction not provided
07 (X,Y,Z): (3373,1037,15); Scored tree; Manual reconstruction not provided
08 (X,Y,Z): (3513,1382,20); Scored tree; Manual reconstruction not provided
09 (X,Y,Z): (2045,547,5); Scored tree; Manual reconstruction not provided
10 (X,Y,Z): (1452,832,22); Scored tree; Manual reconstruction not provided
11 (X,Y,Z): (2938,1533,25); Scored tree; Manual reconstruction not provided
12 (X,Y,Z): (589,1871,26); Scored tree; Manual reconstruction not provided
13 (X,Y,Z): (866,2066,30); Scored tree; Manual reconstruction not provided
14 (X,Y,Z): (3262,1263,92); Scored tree; Manual reconstruction not provided
Section_05
01 (X,Y,Z): (2710,281,6); Scored tree; Manual reconstruction not provided
02 (X,Y,Z): (3534,1073,10); Scored tree; Manual reconstruction not provided
03 (X,Y,Z): (2725,1126,13); Scored tree; Manual reconstruction not provided
04 (X,Y,Z): (1885,703,5); Scored tree; Manual reconstruction not provided
05 (X,Y,Z): (1152,1174,12); Scored tree; Manual reconstruction not provided
06 (X,Y,Z): (336,1985,13); Scored tree; Manual reconstruction not provided