NWB files used

This sections lists the NWB files used for the speed_check.py utility example run which has partial output given in the previous section. The files used are:

  • File: Steinmetz2019_Forssmann_2017-11-05.nwb (267.96 MB). From an NWB-formatted dataset referenced in Steinmetz et al. Nature 2019. Available at: https://figshare.com/articles/Datasets_from_Steinmetz_et_al_2019_in_NWB_format/11274968 MD5: fc4052bffd3c2f4cf8d42f000696348c

  • A data file from Buzsaki Lab. File: YutaMouse41-150903.nwb (10 GB). It is available from https://buzsakilab.nyumc.org/datasets/NWB/SenzaiNeuron2017/ MD5: 3dd2251ba2c61abb9edae1117bbaecf0

  • The first 16 files from the alm-1 data set at CRCNS.org, which contains anterior motor cortex recordings from the Svoboda Lab at Janelia Farm. (Total 2.2 GB). Available from: http://crcns.org/data-sets/motor-cortex/alm-1 MD5 sums are listed with the files at CRCNS.org.

  • Files in file nwb_1_28.zip from the Anne K Churchland lab.17 (28 files, 17 GB). Available from: http://labshare.cshl.edu/shares/library/repository/37693/ MD5: b9890ad36b7721a1b1c921289f19c698

  • Files generated from the PyNWB tutorials. (22 files, 542 MB total). The tutorials (Python code to generate the files) are at: https://pynwb.readthedocs.io/en/latest/tutorials/index.html The version of the tutorials used here was from commit 4f054b87 (which was the latest on Dec 27, 2019). Steps for generating the same version of the files are:

    git clone --recurse-submodules https://github.com/NeurodataWithoutBorders/pynwb.git

    cd pynwb

    git log --oneline -1

    If output is NOT:

    4f054b87 (HEAD -> dev, tag: latest, origin/dev, origin/HEAD) Update legacy import of ObjectMapper (#1124)

    then do:

    git checkout 4f054b87

    (To checkout the version of PyNWB used to generate the version of the NWB files used in the speed_check.py run). Once the proper version of PyNWB is checked-out, do:

    pip install -r requirements.txt

    pip install .

    cd docs/gallery/general

    python file.py

    (The ‘python’ command generates file example_file_path.nwb). To generate the other NWB files, run the python command on the other .py files in both general and the “gallery/domain” directory. (In directory “general” files: advanced_hdf5_io.py, extensions.py, iterative_write.py, linking_data.py, scratch.py); in directory “domain” files: ecephys.py, icephys.py, ophys.py, and brain_observatory.py). A total of 24 NWB files should be generated. They are included in the list below.

The list of files (in the index file, e.g. nwb_index.db) used in the speed_check.py example run is given below. This list was displayed by running the query_index.py program in interactive mode in the directory containing file nwb_index.db.

$ query_nwbindex ./
Using index_path: './nwb_index.db'
Opening './nwb_index.db'
Searching 70 files:
1. ./Steinmetz2019_Forssmann_2017-11-05.nwb
2. ./YutaMouse41-150903.nwb
3. ./alm-1/data_structure_ANM210861_20130701.nwb
4. ./alm-1/data_structure_ANM210861_20130702.nwb
5. ./alm-1/data_structure_ANM210861_20130703.nwb
6. ./alm-1/data_structure_ANM210862_20130626.nwb
7. ./alm-1/data_structure_ANM210862_20130627.nwb
8. ./alm-1/data_structure_ANM210862_20130628.nwb
9. ./alm-1/data_structure_ANM210863_20130626.nwb
10. ./alm-1/data_structure_ANM210863_20130627.nwb
11. ./alm-1/data_structure_ANM210863_20130628.nwb
12. ./alm-1/data_structure_ANM214427_20130805.nwb
13. ./alm-1/data_structure_ANM214427_20130806.nwb
14. ./alm-1/data_structure_ANM214427_20130807.nwb
15. ./alm-1/data_structure_ANM214427_20130808.nwb
16. ./alm-1/data_structure_ANM214429_20130805.nwb
17. ./alm-1/data_structure_ANM214429_20130806.nwb
18. ./alm-1/data_structure_ANM214429_20130807.nwb
19. ./churchland/mouse1_fni16_150817_001_ch2-PnevPanResults-170808-190057.nwb
20. ./churchland/mouse1_fni16_150818_001_ch2-PnevPanResults-170808-180842.nwb
21. ./churchland/mouse1_fni16_150819_001_ch2-PnevPanResults-170815-163235.nwb
22. ./churchland/mouse1_fni16_150820_001_ch2-PnevPanResults-170808-185044.nwb
23. ./churchland/mouse1_fni16_150821_001-002_ch2-PnevPanResults-170808-184141.nwb
24. ./churchland/mouse1_fni16_150825_001-002-003_ch2-PnevPanResults-170814-191401.nwb
25. ./churchland/mouse1_fni16_150826_001_ch2-PnevPanResults-170808-002053.nwb
26. ./churchland/mouse1_fni16_150827_001_ch2-PnevPanResults-170807-171156.nwb
27. ./churchland/mouse1_fni16_150828_001-002_ch2-PnevPanResults-170807-204746.nwb
28. ./churchland/mouse1_fni16_150831_001-002_ch2-PnevPanResults-170807-193348.nwb
29. ./churchland/mouse1_fni16_150901_001_ch2-PnevPanResults-170807-072732.nwb
30. ./churchland/mouse1_fni16_150903_001_ch2-PnevPanResults-170809-075033.nwb
31. ./churchland/mouse1_fni16_150904_001_ch2-PnevPanResults-170809-073123.nwb
32. ./churchland/mouse1_fni16_150915_001_ch2-PnevPanResults-170806-163508.nwb
33. ./churchland/mouse1_fni16_150916_001-002_ch2-PnevPanResults-170806-114920.nwb
34. ./churchland/mouse1_fni16_150917_001_ch2-PnevPanResults-170806-110934.nwb
35. ./churchland/mouse1_fni16_150918_001-002-003-004_ch2-PnevPanResults-170715-124821.nwb
36. ./churchland/mouse1_fni16_150921_001_ch2-PnevPanResults-170715-114212.nwb
37. ./churchland/mouse1_fni16_150922_001_ch2-PnevPanResults-170715-120548.nwb
38. ./churchland/mouse1_fni16_150923_001_ch2-PnevPanResults-170715-124558.nwb
39. ./churchland/mouse1_fni16_150924_001_ch2-PnevPanResults-170715-124619.nwb
40. ./churchland/mouse1_fni16_150925_001-002-003_ch2-PnevPanResults-170715-164713.nwb
41. ./churchland/mouse1_fni16_150928_001-002_ch2-PnevPanResults-170716-002540.nwb
42. ./churchland/mouse1_fni16_150929_001-002_ch2-PnevPanResults-170715-205011.nwb
43. ./churchland/mouse1_fni16_150930_001-002_ch2-PnevPanResults-161221-134921.nwb
44. ./churchland/mouse1_fni16_151001_001_ch2-PnevPanResults-161220-141515.nwb
45. ./churchland/mouse1_fni16_151002_001-002_ch2-PnevPanResults-161221-152112.nwb
46. ./churchland/mouse1_fni16_151005_001-002-003-004_ch2-PnevPanResults-161221-150439.nwb
47. ./tutorials/domain/brain_observatory.nwb
48. ./tutorials/domain/ecephys_example.nwb
49. ./tutorials/domain/icephys_example.nwb
50. ./tutorials/domain/ophys_example.nwb
51. ./tutorials/general/advanced_io_example.nwb
52. ./tutorials/general/basic_alternative_custom_write.nwb
53. ./tutorials/general/basic_iterwrite_example.nwb
54. ./tutorials/general/basic_sparse_iterwrite_compressed_example.nwb
55. ./tutorials/general/basic_sparse_iterwrite_example.nwb
56. ./tutorials/general/basic_sparse_iterwrite_largearray.nwb
57. ./tutorials/general/basic_sparse_iterwrite_largechunks_compressed_example.nwb
58. ./tutorials/general/basic_sparse_iterwrite_largechunks_example.nwb
59. ./tutorials/general/basic_sparse_iterwrite_multifile.nwb
60. ./tutorials/general/cache_spec_example.nwb
61. ./tutorials/general/example_file_path.nwb
62. ./tutorials/general/external1_example.nwb
63. ./tutorials/general/external2_example.nwb
64. ./tutorials/general/external_linkcontainer_example.nwb
65. ./tutorials/general/external_linkdataset_example.nwb
66. ./tutorials/general/processed_data.nwb
67. ./tutorials/general/raw_data.nwb
68. ./tutorials/general/scratch_analysis.nwb
69. ./tutorials/general/test_cortical_surface.nwb
70. ./tutorials/general/test_multicontainerinterface.nwb
Enter query, control-d to quit