Skip to content
This repository has been archived by the owner on Mar 13, 2023. It is now read-only.

Latest commit

 

History

History
160 lines (120 loc) · 7.82 KB

README.md

File metadata and controls

160 lines (120 loc) · 7.82 KB
Raw

Janelia Research Campus

jrc_logo_180x40

Copyright (c) 2017, HHMI-Janelia Research Campus All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright
  notice, this list of conditions and the following disclaimer.
  
* Redistributions in binary form must reproduce the above copyright
  notice, this list of conditions and the following disclaimer in the
  documentation and/or other materials provided with the distribution.
  
* Neither the name HHMI-Janelia Research Campus nor the
  names of its contributors may be used to endorse or promote products
  derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL HHMI-JANELIA RESEARCH CAMPUS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Contributor: Gennady Denisov

Acknowledgements: Karel Svoboda, Diego Gutnisky and Jeff Teeters

Introduction

According to the NWB API specification,

https://github.com/NeurodataWithoutBorders/specification/blob/master/version_1.0.5_beta/NWB_file_format_specification_1.0.5g_beta.pdf,

NWB data format is a HDF5 format with neurophysiology data-specific structure of groups and datasets. In particular, at the top level of a NWB file, six groups with required/fixed names must be present ("acquisition", "analysis", "epochs", "general", "processing" and "stimulus"), together with several datasets, all of them also with required names. The top groups contain other (nested) groups and datasets, some of them also possessing required names, and others possessing user-specified names, depending on particular data.

The Python framework stored in this folder implements next generation approach to practical conversion of experimental neurophysiology data from their original formats to the NWB format: EXP => NWB. The approach is expected to facilitate the conversion procedure from any original format, although will require partial re-implementation for new input data.

exp2nwb_flowchart_new

The distinctive features of this approach are:

  • decomposition of the conversion project NWB file into a set of "elementary" tasks, each of which can be performed independently. Each the task will produce a partial NWB file, where only a certain group or subset of nested groups of the target NWB file will be created and populated with datasets, while the rest of the groups and datasets are either missing or empty;
  • further decomposition of each the "elementary" task in two steps:
    1. (exp2dict): extract a relavant portion of experimental data from input file(s) and store it in a Python dictionary. The keys in this dictionary will be the full paths to datasets or attributes in the target NWB file, and the values will be the contents of the datasets or attributes; and
    2. (dict2nwb): given a dictionary generated for a given task, produce the corresponding partial NWB file.
  • each the partial NWB file thus produced is named accordingly with the portion of data it contains, is stored in a project directory and can be subsequently reviewed using an HDF viewer. For example, the partial NWB file where only data in the group "/general/subject" are populated will be named "general.subject.h5".
  • after all the required partial NWB files have been produced, the final, full-size NWB file will be generated in one step via assembly of the partial files.

The exact set of the partial NWB files to be produced will depend on the type of the data being converted. Depending on the data, some of the partial files may or may not be produced. We discriminate between two major types of neurophysiology data:

  1. electrophysiology ("ephys") data, where the brain activity is recorded using either extracellular or intracellular electrode probes (or both); and
  2. optophysiology ("ophys") data, where the brain activity is recorded using calcium fluirescence imaging.

The functions in the library dict2nwb are expected to be "standard", i.e. not to change from one dataset to another, whreas the functions in the library exp2dict should be re-implemented in conjunction with domain scientists, depending on their data.

As a sample, we provide implementation of exp2dict.py for two datasets, both generated at Svoboda lab in Janelia and uploaded to the crcns.org website:

  • ephys dataset (Li et al, Nature 2015, doi: 10.1038/nature14178),

    https://portal.nersc.gov/project/crcns/download/alm-1     

https://portal.nersc.gov/project/crcns/download/alm-2

and

  • ophys datsets (Peron et al, Neuron 2015, doi: 10.1016/j.neuron.2015.03.027)

    https://portal.nersc.gov/project/crcns/download/ssc-1

A list of dictionary keys that are exoected to be defined when re-implementing the functions in library exp2dict is provided in doc/README_exp2dict_keys.

Code usage

The code comprises a script exp2nwb.py together with three library files: libexp2dict.py, libdict2nwb.py and util.py. Given a processing string , the script employs a function from the library libexp2dict.py to create a dictionary for each particular task and then, given the dictionary, a function from the library libdict2nwb.py to create a particual NWB file .h5. The names of these functions are typically the same for the two libraries and match the processing string, but with "dots" replaced by "underscore" symbols. The library util.py have been employed by functions in libexp2dict.py in order to extract data from input file(s).

For the two datasets mentioned above, the full sets of supported p-strings is listed in doc/README_p-strings.

The current implementation of both exp2nwb.py and libexp2dict.py assumes the imput data files are in the HDF5 format. The experimental data at are actually stored in MAT format, can be converted to HDF5 format using our script https://github.com/NeurodataWithoutBorders/mat2nwb/blob/master/mat2h5.py

To see the usage of the script exp2nwb.py, type the name of the script:

$ exp2nwb.py

Usage: exp2nwb.py .h5 [ <meta_data>.h5] [options (-h to list)]

All the available command line options can be viewed by typing

$ exp2nwb.py -h

In particular, to produce a single partial NWB file .h5 from the input data, type

$ exp2nwb.py <data>.h5 [ <meta_data>.h5]  -s <pstring> -d <project_folder>

The partial NWB file will be stored in the project folder <project_folder>, which, by default, has the same name as .

To assemble all the partial NWB files in folder <project_folder>, type

$ exp2nwb.py <project_folder>.

This command will produce a full NWB file named, by default, <project_folder>.nwb, or the name spwcified by the option "-o <output_file>".

After the assembly, the project folder will be deleted by default, unless the debugging mode has been used, as specified by the option "-D".