Greene et al., Cell Reports 2015
The file is a 6G tar-gz archive. Decompressed, it is approximately 34G.
Contained are raw files, one for each reconstructed cell. They are placed in subfolders corresponding to their cell type.
Each file is named in the form of “cXXXXX.raw”. The files are uint32 encoded binary data files consisting of n*3 values, where n is the number of voxels comprising the cell. The values within the file correspond to the (z, x, y) coordinates of the voxel in the volume, in that order. The z-axis is defined as the light axis.
E.g. the first three values in the file “./BC1/c60008.raw” are the z, then x, then y coordinate of the first voxel that is part of the cell with ID 60008, which is a type 1 Bipolar Cell. The next three values are the coordinates for the next voxel and so forth. There is no particular ordering for the voxels.
Lee et al, NIPS 2015 Training Data
The above file contains the training dataset used for our piriform cortex studies, by Kisuk Lee and Ashwin Vishwanathan.
Kim et al, Nature 2014 Reconstruction Data
Here you can find reconstruction data of bipolar cells (BCs) and Starburst Amacrine Cells (SACs) covered in our paper, Kim et al, Nature 2014. The data is volume segmentation in the format of indexed image, where each voxel of the 3D image is labeled by a cell ID. The dimension of the 3D image is 2432 x 10496 x 6528 voxels. It was down-sampled by factor of 2 from the original data due to the magnitude, but the resolution is still high enough to analyze the ultra-fine structure of neurons and the contacts between them. The effective voxel size is 33 x 33 x 46 nm per voxel. The file is stored in uint32 raw linear format with 128 x 128 x 128 voxel “chunks”. Below is a MATLAB sample code to read the (9,31,20)-th chunk, or equivalently the chunk at (1025~1152, 3841~3968, 2433~2560).
size_of_volume=[2432 10496 6528]; size_of_chunk=[128 128 128]; volume_size_in_chunk=size_of_volume./size_of_chunk; linear_size_of_chunk=prod(size_of_chunk); sub_chunk={9 31 20}; idx_chunk=sub2ind(volume_size_in_chunk,sub_chunk{:}); offset=4*(idx_chunk-1)*linear_size_of_chunk; f=fopen(segmentation_file_name,'r'); fseek(f,offset,'bof'); chunk=reshape(fread(f,linear_size_of_chunk,'*uint32'),size_of_chunk); fclose(f);
Caution: The file size of original file is 621GB when it is uncompressed (839MB compressed). Secure disk space accordingly before you work with the data. Cell ID by Neuron Types:
Off SAC 70016 70023 70024 70025 70026 70027 70030 70031 70033 70035 70048 70050 70066 70079 70080 70081 70082 70083 70085 70086 70087 70088 70089 70090 70093 70095 70096 70099 70100 70102 70108 70133 70134 70137 70138 70141 70145 70146 70147 70148 70149 70150 70151 70152 70154 70155 70156 70158 70034 70131 70106 70110 70126 70014 70032 70068 70076 70077 70084 70109 70111 70112 70113 70114 70115 70116 70117 70118 70119 70120 70121 70122 70123 70124 70125 70127 70128 70129 70130 BC1 60008 60019 60026 60027 60032 60052 60055 60078 60079 60099 60105 60109 60110 60111 60114 60118 60129 60132 60139 60142 60147 60150 60158 60161 60162 60164 60170 60177 60184 60187 60188 60189 60194 60195 60196 60203 60204 60212 60213 60216 60218 60227 BC2 60001 60002 60003 60004 60006 60009 60010 60011 60012 60013 60021 60022 60023 60025 60029 60037 60038 60039 60040 60041 60042 60043 60044 60046 60080 60097 60101 60102 60103 60104 60112 60120 60124 60130 60133 60135 60138 60140 60141 60149 60157 60159 60167 60169 60182 60198 60208 60209 60210 60214 60217 60219 60221 60223 60224 60226 BC3a 60093 60092 60145 60108 60059 60181 60137 60123 60176 60115 60028 60146 60136 60066 60076 60172 60048 60050 60166 60088 60072 60068 60134 60085 60049 60056 60075 60030 BC3b 60096 60151 60131 60094 60090 60069 60215 60045 60024 60063 60228 60154 60122 60081 60087 60173 60201 60084 60057 60106 60073 60178 60156 60107 60211 60165 60077 60153 60082 60053 60190 60148 60074 60098 60179 BC4 60089 60083 60119 60163 60095 60186 60160 60191 60171 60144 60222 60117 60202 60058 60067 60125 60116 60168 60047 60121 60183 60086 60206 60175 60091 60197 60100 60143 60127 60185 60199 60220 60174