Utilities to look at widefield data and align with the allen reference map.
wfield - tools to analysis widefield data
This is a python package for visualizing and analysing data collected with a widefield macroscope.
Use the graphical interface to launch analysis on NeuroCAAS
These tools are for:
- Motion correction
- Data reduction
- Hemodynamic correction
- Matching to the Allen CCF
- Visualize raw/reduced data and ROIs
Use cases and instructions here
A dataset that can be used to demo some of the functionality of this repository will be made available in the
File format conventions
raw frame data, when stored in binary files (uint16)
the filename must end with:
Example: "frames_2_540_640_uint16.dat" H and W are the dimensions of a single frame.
These files can be opened with the command
wfield open_raw <filename>
denoised/decomposed (locally processed) data are stored as
U.npyare the spatial components
(H, W, NCOMPONENTS)
SVT.npyare the temporal components
SVTcorr.npyis the hemodynamic corrected temporal components
info.jsonhas information about the dataset like the
NeuroCAAS results folder
U_atlas.npyare the spatial components transformed to a common atlas reference frame.
(H, W, NCOMPONENTS)
reduced_spatial.npyare the spatial components from the PMD
The H and W of the matrix are in the
config.yamlfile (or use
SVTcorr.npyare the hemodynamic corrected temporal components
reduced_temporal.npyare the temporal components for the first channel `(NCOMPONENTS, NFRAMES)
- LocaNMF returns a matlab file with components in spatial components in the
Avariable and temporal components in the
Installation (from pip)
pip install wfield
Installation (using Anaconda)
To install start by getting Anaconda or Miniconda. Install also git. Run the following commands from a terminal window (Anaconda prompt or git Bash on Windows, the Mac OS terminal). Check the notes below for common issues.
Go to the folder where you want to install and clone the repository:
git clone https://github.com/jcouto/wfield.git. This creates a directory; go inside that directory:
cd wfield. Alternatively you can download the repository as a [zip file] (https://github.com/churchlandlab/wfield/archive/master.zip).
Use anaconda to install all dependencies:
conda env create -f env.ymlthe file env.yml is inside the
Enter the environment
conda activate wfieldand install wfield using the command
python setup.py installfollowed by
python setup.py references
You will need to run
conda activate wfieldto activate the environment before running the software every time you start a terminal.
You are all set.
wfield -hto see the available commands.
Go here for instructions on how to use NeuroCAAS.
Note: Some reference files used to match to the Allen Common Coordinate Framework are copied from the folder references to
$HOME/.wfield during installation.
Note for Mac users:
gitwhen you try the instructions you will be asked to install git, if that fails you can run
conda install gitto install using anaconda.
Note for Windows users:
- Get a terminal like git bash [optional]
conda init bashto activate conda on
- When you install Anaconda, set the option to install as system python (this makes that it is visible from the terminal without having to run the Anaconda Prompt).
Note for developers: In some cases you may want to make changes to the software, if you need this run
python setup.py develop (you can not move the folder after this - the installation will point to that directory).
The software was tested on Windows, Linux and MacOS Catalina. Installation takes less than 5 minutes on a standard computer with fast access to internet and a previous anaconda installation.
Instructions to use with NeuroCAAS here.
There is a command-line inteface to run computations from the command line. Do
wfield -h to learn more.
Notebook examples are here.
Look at this one to load decomposed data and extract ROIs.
Copyright (C) 2020 Joao Couto - firstname.lastname@example.org
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
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