The Data Sets - Neuromuscular Projection Fibers
Folder Contents:
This is 1 of the 5 datasets used for the DIADEM Grand Challenge Qualifiers Round.
This dataset consists of 12 separate mouse neuromuscular axonal projection fibers all contained within the same 152 image stacks. Each image stack represents one tile for a montage that contains all 12 separate axonal projections. Thus, all image stacks are to be used for both training and scored projections. Manual reconstructions are provided for 6 of these 12 axonal trees, which are to be used as templates for training (see 'General README'). Contestants will trace the other 6 trees which will be officially scored for the Qualifiers Round.
Experimental Procedures:
Dataset owner: JW Lichtman, Department of Molecular and Cellular Biology, Harvard University
Species: Mouse
Strain: Thy1-Brainbow-1 Line B
Nervous System Region: Peripheral
Fiber type: Axons
Labeling Method: Brainbow
Image Acquisition Method: 2-channel confocal microscopy
Tracing Method: Reconstruct/NeuronJ
Objective Lens: 20x (0.8 NA), 40x (1.3 NA), or 60x (1.45 NA) oil
See Lu et al., 2009, PLoS Biol. 7(2):e32 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 'Neuromuscular Projection Fibers Part_1.rar' through
'Neuromuscular Projection Fibers Part_7.rar'.
2. 'Neuromuscular Projection Fibers Part_1.rar' contains the subfolder
'Manual Reconstructions', whereas 'Neuromuscular Projection Fibers
Part_2.rar' through 'Neuromuscular Projection Fibers Part_7.rar' contain
image stacks.
3. There will be 152 total image stacks that when tiled together contain all
12 neuromuscular projection fibers.
4. Unlike some other datasets, image stack numbers do not correspond to
reconstruction numbers, since all reconstructions use the same image stacks
(though a given image stack may or may not contain portions of each of the 12
neuromuscular projection fibers).
5. 'Manual Reconstructions' folder will contain 6 SWC files: 'NM_01' through
'NM_06'.
6. The 'Manual Reconstruction' folder contains manually-traced digital
reconstructions (in SWC format) that were traced in 3 dimensions (X,Y, and Z)
as provided by the corresponding data provider, but were collapsed in the Z
dimension to produce 2-dimensional reconstructions. Thus, contestants can use
Z information to aid in reconstruction method, but actual Z values will be
collapsed by the metric program and not considered in scoring (Note that Z
information is used in all of the other datasets).
7. The name of the top image of each image stack starts with 00, unlike other
datasets, which start with 01. Regardless, the top image Z value still = 0.
Therefore, for this dataset only, Z values are the same as the number
provided in each image's name.
8. Unlike other datasets, SWC files will not automatically align with image
stacks. The 'Translation' section below shows how many pixels in XY a stack
would have to be moved to align with each SWC file. Instructions are provided
under 'Individual Stack Information' below for how to use translation values
when moving the SWC files instead of the image stacks (as must be done in
Neuromantic).
9. Translation coordinate numbers correspond to the position of the top left
corner for each image stack.
10. Z translation values are not provided. It is not necessary to know Z
values, since Z information will be collapsed. However, it may be helpful to
know relative Z position of structures within neighboring image stacks to
decide how to connect them. If needed for aligning image stack tiles,
relative Z values can be obtained by going through each image stack and
seeing where overlapping structures are in focus.
11. Most image stacks contain ~10% overlap, but some of them overlap much
more. Overlapping structures should only be traced once.
12. Starting coordinates are given below that clearly mark the root of the
correct axonal projections to reconstruct.
13. Assuming that contestants reconstruct from each image stack separately,
finished reconstructions that cross multiple image stacks must be connected
into single trees as is done for the provided manual reconstructions.
14. Alternatively, software such as VIAS
(http://mssm.edu/cnic/tools-vias.html) can be used to tile and integrate
stacks into unified image stacks, but the dataset size may then become too
large to load all image stacks integrated together. Note: While VIAS can be
used to integrate image stacks with structures collapsed into single 2D
images, it is advised to use the individual image stacks for tracing since
some overlapping stacks do not contain the same structures due to differences
in Z depth range.
15. Special Note for this dataset only: As observed in the training SWC files provided, branch terminations are typically not traced to their furthest extent. Branch terminations typically end as convoluted or bulbous arborizations known as 'rosettes'. Because rosette roots and terminations are unclear, terminating later along a branch than the manual reconstruction, or even bifurcating, will not be counted against the score. Terminating too early may count against the score if the termination is outside of the manual reconstruction termination's Euclidean distance threshold.
Manual Reconstruction NM_1 (blue) is superimposed over image stack NM_111. The root of the reconstruction is outside the image borders.
Individual Stack Information (all image stacks are 1024x1024 pixels in XY): The values below describe how far to move image stacks when they load at (X,Y) = (0,0) at the upper left corner of the image stack. If using Neuromantic, which does not have an option to translate image stacks, the reconstructions must instead be moved by the negative of each image stack's X and Y values below to align properly with that image stack.
NM_01- Number of images: 201; Translation (X,Y): (7694,0)
NM_02- Number of images: 205; Translation (X,Y): (9504,6)
NM_03- Number of images: 94; Translation (X,Y): (10410,10)
NM_04- Number of images: 46; Translation (X,Y): (13104,4)
NM_05- Number of images: 214; Translation (X,Y): (7686,922)
NM_06- Number of images: 213; Translation (X,Y): (8592,926)
NM_07- Number of images: 211; Translation (X,Y): (9496,930)
NM_08- Number of images: 119; Translation (X,Y): (10400,934)
NM_09- Number of images: 111; Translation (X,Y): (13120,940)
NM_10- Number of images: 111; Translation (X,Y): (14022,944)
NM_11- Number of images: 106; Translation (X,Y): (14926,946)
NM_12- Number of images: 162; Translation (X,Y): (2254,1866)
NM_13- Number of images: 163; Translation (X,Y): (3164,1998)
NM_14- Number of images: 140; Translation (X,Y): (4066,2106)
NM_15- Number of images: 188; Translation (X,Y): (4966,1834)
NM_16- Number of images: 65; Translation (X,Y): (5866,1838)
NM_17- Number of images: 212; Translation (X,Y): (8578,1846)
NM_18- Number of images: 207; Translation (X,Y): (9486,1852)
NM_19- Number of images: 125; Translation (X,Y): (10394,1854)
NM_20- Number of images: 193; Translation (X,Y): (13112,1864)
NM_21- Number of images: 149; Translation (X,Y): (14014,1866)
NM_22- Number of images: 143; Translation (X,Y): (14914,1868)
NM_23- Number of images: 57; Translation (X,Y): (4960,2756)
NM_24- Number of images: 79; Translation (X,Y): (4540,2456)
NM_25- Number of images: 176; Translation (X,Y): (5860,2758)
NM_26- Number of images: 103; Translation (X,Y): (6766,2714)
NM_27- Number of images: 78; Translation (X,Y): (7668,2820)
NM_28- Number of images: 55; Translation (X,Y): (8572,2730)
NM_29- Number of images: 118; Translation (X,Y): (9482,2794)
NM_30- Number of images: 104; Translation (X,Y): (10386,2766)
NM_31- Number of images: 149; Translation (X,Y): (12198,2778)
NM_32- Number of images: 207; Translation (X,Y): (13106,2780)
NM_33- Number of images: 197; Translation (X,Y): (14006,2782)
NM_34- Number of images: 167; Translation (X,Y): (14908,2784)
NM_35- Number of images: 53; Translation (X,Y): (4954,3670)
NM_36- Number of images: 145; Translation (X,Y): (5858,3674)
NM_37- Number of images: 159; Translation (X,Y): (6766,3676)
NM_38- Number of images: 77; Translation (X,Y): (7666,3678)
NM_39- Number of images: 71; Translation (X,Y): (8570,3680)
NM_40- Number of images: 62; Translation (X,Y): (9480,3684)
NM_41- Number of images: 159; Translation (X,Y): (10384,3686)
NM_42- Number of images: 163; Translation (X,Y): (11288,3690)
NM_43- Number of images: 110; Translation (X,Y): (12194,3692)
NM_44- Number of images: 93; Translation (X,Y): (13100,3694)
NM_45- Number of images: 203; Translation (X,Y): (14000,3696)
NM_46- Number of images: 208; Translation (X,Y): (14902,3698)
NM_47- Number of images: 103; Translation (X,Y): (6754,4586)
NM_48- Number of images: 71; Translation (X,Y): (8568,4592)
NM_49- Number of images: 82; Translation (X,Y): (9472,4596)
NM_50- Number of images: 123; Translation (X,Y): (10380,4600)
NM_51- Number of images: 135; Translation (X,Y): (11286,4602)
NM_52- Number of images: 75; Translation (X,Y): (13094,4606)
NM_53- Number of images: 168; Translation (X,Y): (13994,4608)
NM_54- Number of images: 111; Translation (X,Y): (14894,4610)
NM_55- Number of images: 34; Translation (X,Y): (15802,4616)
NM_56- Number of images: 102; Translation (X,Y): (6760,5520)
NM_57- Number of images: 73; Translation (X,Y): (9470,5510)
NM_58- Number of images: 127; Translation (X,Y): (10374,5512)
NM_59- Number of images: 148; Translation (X,Y): (11280,5516)
NM_60- Number of images: 19; Translation (X,Y): (11268,5508)
NM_61- Number of images: 112; Translation (X,Y): (12180,5518)
NM_62- Number of images: 93; Translation (X,Y): (13086,5520)
NM_63- Number of images: 92; Translation (X,Y): (13988,5520)
NM_64- Number of images: 126; Translation (X,Y): (14892,5524)
NM_65- Number of images: 154; Translation (X,Y): (15794,5526)
NM_66- Number of images: 125; Translation (X,Y): (16698,5528)
NM_67- Number of images: 44; Translation (X,Y): (6750,6438)
NM_68- Number of images: 55; Translation (X,Y): (7200,5942)
NM_69- Number of images: 59; Translation (X,Y): (7656,6440)
NM_70- Number of images: 67; Translation (X,Y): (10368,6430)
NM_71- Number of images: 153; Translation (X,Y): (11272,6438)
NM_72- Number of images: 150; Translation (X,Y): (12174,6442)
NM_73- Number of images: 122; Translation (X,Y): (13080,6444)
NM_74- Number of images: 115; Translation (X,Y): (13982,6442)
NM_75- Number of images: 125; Translation (X,Y): (14882,6444)
NM_76- Number of images: 151; Translation (X,Y): (15786,6448)
NM_77- Number of images: 93; Translation (X,Y): (16690,6450)
NM_78- Number of images: 67; Translation (X,Y): (17594,6452)
NM_79- Number of images: 47; Translation (X,Y): (18500,6454)
NM_80- Number of images: 68; Translation (X,Y): (7650,7362)
NM_81- Number of images: 43; Translation (X,Y): (9452,7348)
NM_82- Number of images: 77; Translation (X,Y): (10362,7350)
NM_83- Number of images: 59; Translation (X,Y): (11266,7358)
NM_84- Number of images: 76; Translation (X,Y): (12166,7362)
NM_85- Number of images: 78; Translation (X,Y): (13084,7374)
NM_86- Number of images: 63; Translation (X,Y): (13978,7360)
NM_87- Number of images: 152; Translation (X,Y): (14878,7362)
NM_88- Number of images: 119; Translation (X,Y): (15778,7368)
NM_89- Number of images: 159; Translation (X,Y): (16680,7370)
NM_90- Number of images: 108; Translation (X,Y): (17590,7372)
NM_91- Number of images: 65; Translation (X,Y): (18494,7374)
NM_92- Number of images: 100; Translation (X,Y): (5834,8286)
NM_93- Number of images: 129; Translation (X,Y): (6736,8288)
NM_94- Number of images: 85; Translation (X,Y): (7642,8288)
NM_95- Number of images: 45; Translation (X,Y): (8546,8290)
NM_96- Number of images: 30; Translation (X,Y): (9454,8292)
NM_97- Number of images: 105; Translation (X,Y): (10438,8354)
NM_98- Number of images: 36; Translation (X,Y): (13076,8306)
NM_99- Number of images: 115; Translation (X,Y): (13968,8290)
NM_100- Number of images: 131; Translation (X,Y): (14872,8292)
NM_101- Number of images: 147; Translation (X,Y): (15774,8294)
NM_102- Number of images: 134; Translation (X,Y): (16674,8300)
NM_103- Number of images: 134; Translation (X,Y): (17580,8302)
NM_104- Number of images: 65; Translation (X,Y): (17578,8264)
NM_105- Number of images: 41; Translation (X,Y): (5828,9206)
NM_106- Number of images: 85; Translation (X,Y): (6732,9202)
NM_107- Number of images: 109; Translation (X,Y): (7634,9206)
NM_108- Number of images: 49; Translation (X,Y): (8540,9210)
NM_109- Number of images: 63; Translation (X,Y): (9444,9210)
NM_110- Number of images: 100; Translation (X,Y): (13964,9208)
NM_111- Number of images: 130; Translation (X,Y): (14864,9212)
NM_112- Number of images: 137; Translation (X,Y): (15766,9212)
NM_113- Number of images: 50; Translation (X,Y): (16668,9214)
NM_114- Number of images: 114; Translation (X,Y): (6724,10122)
NM_115- Number of images: 151; Translation (X,Y): (7626,10126)
NM_116- Number of images: 75; Translation (X,Y): (7604,10116)
NM_117- Number of images: 102; Translation (X,Y): (8530,10130)
NM_118- Number of images: 32; Translation (X,Y): (8530,10104)
NM_119- Number of images: 88; Translation (X,Y): (9436,10132)
NM_120- Number of images: 176; Translation (X,Y): (14858,10132)
NM_121- Number of images: 192; Translation (X,Y): (15760,10134)
NM_122- Number of images: 139; Translation (X,Y): (16664,10136)
NM_123- Number of images: 108; Translation (X,Y): (17566,10138)
NM_124- Number of images: 23; Translation (X,Y): (17570,10122)
NM_125- Number of images: 67; Translation (X,Y): (18472,10140)
NM_126- Number of images: 138; Translation (X,Y): (6716,11046)
NM_127- Number of images: 122; Translation (X,Y): (7620,11048)
NM_128- Number of images: 97; Translation (X,Y): (8524,11052)
NM_129- Number of images: 51; Translation (X,Y): (9432,11056)
NM_130- Number of images: 66; Translation (X,Y): (10342,11060)
NM_131- Number of images: 186; Translation (X,Y): (14854,11056)
NM_132- Number of images: 193; Translation (X,Y): (15754,11058)
NM_133- Number of images: 102; Translation (X,Y): (7618,11964)
NM_134- Number of images: 117; Translation (X,Y): (8522,11968)
NM_135- Number of images: 54; Translation (X,Y): (9428,11970)
NM_136- Number of images: 61; Translation (X,Y): (10334,11976)
NM_137- Number of images: 152; Translation (X,Y): (15746,11974)
NM_138- Number of images: 67; Translation (X,Y): (16652,11976)
NM_139- Number of images: 74; Translation (X,Y): (8516,12878)
NM_140- Number of images: 85; Translation (X,Y): (9418,12880)
NM_141- Number of images: 115; Translation (X,Y): (9412,13796)
NM_142- Number of images: 175; Translation (X,Y): (2258,2754)
NM_143- Number of images: 139; Translation (X,Y): (1306,3682)
NM_144- Number of images: 131; Translation (X,Y): (800,4600)
NM_145- Number of images: 110; Translation (X,Y): (416,5524)
NM_146- Number of images: 63; Translation (X,Y): (252,6446)
NM_147- Number of images: 64; Translation (X,Y): (0,7382)
NM_148- Number of images: 67; Translation (X,Y): (1336,2772)
NM_149- Number of images: 57; Translation (X,Y): (19400,7378)
NM_150- Number of images: 53; Translation (X,Y): (20298,6886)
NM_151- Number of images: 26; Translation (X,Y): (21262,6876)
NM_152- Number of images: 71; Translation (X,Y): (12554,6636)
Manual Reconstruction Starting Coordinates (X and Y in pixels):
NM_01 (X,Y): (300,8387); Training tree; Manual reconstruction provided
NM_02 (X,Y): (93,8387); Training tree; Manual reconstruction provided
NM_03 (X,Y): (229,8389); Training tree; Manual reconstruction provided
NM_04 (X,Y): (187,8390); Training tree; Manual reconstruction provided
NM_05 (X,Y): (464,8389); Training tree; Manual reconstruction provided
NM_06 (X,Y): (136,8390); Training tree; Manual reconstruction provided
NM_07 (X,Y): (377,8387); Scored tree; Manual reconstruction not provided
NM_08 (X,Y): (243,8388); Scored tree; Manual reconstruction not provided
NM_09 (X,Y): (273,8388); Scored tree; Manual reconstruction not provided
NM_10 (X,Y): (413,8386); Scored tree; Manual reconstruction not provided
NM_11 (X,Y): (324,8385); Scored tree; Manual reconstruction not provided
NM_12 (X,Y): (170,8390); Scored tree; Manual reconstruction not provided