__Folder Contents__:

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

This data set consists of 2 subsets, ‘Subset 1’ and ‘Subset 2’. ‘Subset 1’ and ‘Subset 2’consist of 6 and 10 image stacks, respectively, each containing numerous axonal trees. Each image stack within a subset represents 1 tile for a mosaic that contains all of the separate axonal fibers.

During the DIADEM Grand Challenge Competition: ‘Subset 1’ was used for the Training (01.swc through 14.swc) and Qualifier (15.swc through 34.swc) Rounds and ‘Subset 2’ was used for the Final Round.

__Experimental Procedures__:

Dataset owner: V De Paola, MRC Clinical Sciences Center, Imperial College London

Species: Mouse

Strain: C57/B6, Thy1 transgenic mouse

Nervous System Region: Neocortical layer 1

Fiber type: Axons

Labeling Method: Membrane-targeted GFP in transgenic mouse Line 15

Image Acquisition Method: 2-photon lasers scanning microscopy *in
vivo*

Tracing Method: Neurolucida (Williston, VT)

Objective Lens: 40x water

See De Paola et al., 2006, Neuron Vol 49(6) for general information related to the data

__Z distance between successive images within an image stack__:
3.40 pixels

__Download Instructions__:

1. Download and extract 'Neocortical Layer 1 Axons.rar'.

2. Folder will contain 2 subfolders: ‘Subset 1’ and ‘Subset 2’, which each contain 2 subfolders: 'Image Stacks' and ' Gold Standard Reconstructions'.

3. Subset 1 'Image Stacks' folder will contain 6 subfolders ('01' though '06') each containing 1 of the 6 image stacks. Subset 2 'Image Stacks' folder will contain 10 subfolders ('01' though '10') each containing 1 of the 10 image stacks.

4. Subset 1 ' Gold Standard Reconstructions' folder will contain 34 SWC files: 'NC_01' through 'NC_34'. Subset 2 ' Gold Standard Reconstructions' folder will contain 21 SWC files: 'NC_A' through 'NC_U'.

5. Each SWC file is a manually-traced digital reconstruction traced in 3 dimensions (X,Y, and Z).

6. Gold standard reconstructions use the same image stacks within the given subset (though a given image stack may or may not contain portions of any one of the gold standard reconstructions).

7. SWC files will not automatically align with image stacks when loaded into Neuromantic (except for Subset 1 image stack '06', which happens to have X,Y,Z coordinates = 0,0,0). Instructions are provided under 'Individual Stack Information' below for how to use translation values for proper alignment in X, Y, and Z.

8. Translation coordinate numbers correspond to the position of the top left corner for each image stack.

9. Note that image stack tiles are offset in X, Y, **and Z** unlike for some of the other data sets.

10. Image stack tiles can overlap with each other and can therefore contain redundant structural information.

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

12. Special note for this data set: External branches (i.e. branches that end in a termination) with path lengths of less than 17 pixels will be ignored when using the DIADEM metric. Thus, they can be traced or ignored without affecting the DIADEM metric score, provided that the traced branches remain less than 17 pixels in length.

__Subset 1 Properties:__

__Individual Stack Information (all image stacks are 512x512
pixels in XY and 8 bits per pixel)__: The values below describe how far to move image stacks when they load at (X,Y,Z) = (0,0,0) 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’):**

01- Number of images: 60; Translation (X,Y,Z): (73,507,-5)

02- Number of images: 33; Translation (X,Y,Z): (526,484,11)

03- Number of images: 44; Translation (X,Y,Z): (952,462,-21)

04- Number of images: 51; Translation (X,Y,Z): (924,3,-19)

05- Number of images: 50; Translation (X,Y,Z): (468,-14,-1)

06- Number of images: 46; Translation (X,Y,Z): (0,0,0)

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

NC_1 (X,Y,Z): (1,406,44)

NC_2 (X,Y,Z): (2,143,40)

NC_3 (X,Y,Z): (77,740,20)

NC_4 (X,Y,Z): (77,691,51)

NC_5 (X,Y,Z): (201,1018,48)

NC_6 (X,Y,Z): (560,9,-1)

NC_7 (X,Y,Z): (453,1018,19)

NC_8 (X,Y,Z): (560,230,40)

NC_9 (X,Y,Z): (1,466,25)

NC_10 (X,Y,Z): (109,609,-19)

NC_11 (X,Y,Z): (449,705,54)

NC_12 (X,Y,Z): (365,753,-5)

NC_13 (X,Y,Z): (330,710,-5)

NC_14 (X,Y,Z): (140,1018,39)

NC_15 (X,Y,Z): (435,766,40)

NC_16 (X,Y,Z): (520,607,24)

NC_17 (X,Y,Z): (318,509,10)

NC_18 (X,Y,Z): (1418,971,-9)

NC_19 (X,Y,Z): (1114,913,10

NC_20 (X,Y,Z): (457,252,45)

NC_21 (X,Y,Z): (444,691,-8)

NC_22 (X,Y,Z): (492,279,-1)

NC_23 (X,Y,Z): (522,264,-1)

NC_24 (X,Y,Z): (947,-13,16)

NC_25 (X,Y,Z): (569,329,-1)

NC_26 (X,Y,Z): (1458,462,7)

NC_27 (X,Y,Z): (1110,4,-1)

NC_28 (X,Y,Z): (645,672,47)

NC_29 (X,Y,Z): (1250,420,16)

NC_30 (X,Y,Z): (939,176,14)

NC_31 (X,Y,Z): (1236,65,22)

NC_32 (X,Y,Z): (978,3,23)

NC_33 (X,Y,Z): (1236,4,-5)

NC_34 (X,Y,Z): (994,882,11)

__Subset 2 Properties:__

__Individual Stack Information (all image stacks are 512x512
pixels in XY and 8 bits per pixel)__: The values below describe how far to move image stacks when they load at (X,Y,Z) = (0,0,0) 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’):**

01- Number of images: 77; Translation (X,Y,Z): (1851,749,-22)

02- Number of images: 71; Translation (X,Y,Z): (1857,1192,-7)

03- Number of images: 66; Translation (X,Y,Z): (1345,1202,11)

04- Number of images: 58; Translation (X,Y,Z): (875,1210,18)

05- Number of images: 58; Translation (X,Y,Z): (430,1220,4)

06- Number of images: 67; Translation (X,Y,Z): (62,1227,-10)

07- Number of images: 47; Translation (X,Y,Z): (710,831,17)

08- Number of images: 85; Translation (X,Y,Z): (1145,819,-20)

09- Number of images: 58; Translation (X,Y,Z): (1618,811,7)

10- Number of images: 57; Translation (X,Y,Z): (1401,535,5)

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

NC_A (X,Y,Z): (2034,866,52)

NC_B (X,Y,Z): (1337,821,58)

NC_C (X,Y,Z): (161,1308,28)

NC_D (X,Y,Z): (195,1492,40)

NC_E (X,Y,Z): (1281,821,47)

NC_F (X,Y,Z): (345,1469,29)

NC_G (X,Y,Z): (1929,1698,28)

NC_H (X,Y,Z): (1912,642,45)

NC_I (X,Y,Z): (1378,1305,49)

NC_J (X,Y,Z): (1400,839,-5)

NC_K (X,Y,Z): (2197,1485,29)

NC_L (X,Y,Z): (1296,1441,21)

NC_M (X,Y,Z): (2206,1122,52)

NC_N (X,Y,Z): (1223,1006,12)

NC_O (X,Y,Z): (1357,1283,45)

NC_P (X,Y,Z): (1613,1460,70)

NC_Q (X,Y,Z): (1973,1421,-7)

NC_R (X,Y,Z): (1431,1327,-9)

NC_S (X,Y,Z): (1824,1284,63)

NC_T (X,Y,Z): (1679,1542,12)

NC_U (X,Y,Z): (2050,1703,62)