midesjardins / widefield-imaging-acquisition

A program designed to acquire brain imaging data using intrinsic, GCaMP fluorescence and IR laser speckle optical imaging in awake mice.

Widefield Imaging Acquisition

A Python program to acquire widefield brain images using laser speckle, GCaMP fluorescence and intrinsic optical imaging.
Explore the docs »

Table of Contents

1. About The Project
   • Built With
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. Roadmap
5. Contributing
6. License
7. Contact
8. Acknowledgments

About The Project

There are many Widefield Imaging programs available on the Internet. However, they tend to be unnecessarily complex to use or limited in their capacities. With the present software, we hope to achieve a balance between usability and feature-richness, allowing simple acquisitions as well as complex workflows. Some of the main features of the program are:

• The ability to acquire laser speckle, fluorescence and intrinsic optical imaging at the same time
• The recursive stimulation generation tools, including different signal shapes and support for delay, jitter and repeat
• The support for multiple stimulation channels and their visual rendering
• The visual display of live video channels and activations maps
• ...And much more!

You can download the program by following the instructions below. Some indications are also given on how to adapt the program to your current setup. Note that only National Instruments DAQs and IMAQ-compatible cameras have built-in support. If you want to use other devices, you will need to so some coding on your own.

(back to top)

Built With

Frameworks and libraries used:

• Python
• PyQt5
• Numpy
• Scipy
• Matplotlib
• NIDAQMX
• Pylablib

Physical devices used for testing:

• USB X SERIES Multifunction DAQ
• Dalsa 1M60 (Camera)
• NI PCIe-1427 (Framegrabber)

(back to top)

Getting Started

Prerequisites

• Python 3.9 must be installed

Installation

1. Download the latest release in the Releases section of the repository.
2. Unzip the downloaded file and move to desired location.
3. Install the required modules using one of the following methods:

Using Pip

1. Open a terminal window
2. Go to the directory where the program is saved using the cd command.
3. Run the following command: pip install -r requirements.txt

Using Anaconda

1. Open a terminal window
2. Run the following two commands:

conda create -n py3.9 python=3.9.12
conda activate py3.9

3. In a terminal window, go to the directory where the program is saved using the cd command.
4. Run the following command: pip install -r requirements.txt

(back to top)

Usage

Running the program

1. Launch the interface.py module found in the gui subfolder.

Modifying the DAQ ports

1. Open the config.json file using any text editor.
2. For each type of instrument, replace the port name with the desired name.

Important: Specified ports must exist on DAQ and be of the same type than those specified in the default configuration file. These are respectively:

• Analog Outputs: "analog0", "analog1"
• Digital Outputs: "infrared", "red", "green", "blue", "camera", "co2
• Digital Input: "trigger"

Modifying the Binning

1. Open the config.json file using any text editor.
2. Replace the Binning variable with either 1, 2, 4 or 8

For more examples, please refer to the Documentation

(back to top)

Roadmap

• Release Alpha Version
• Release Beta Version
• Add Progress Line in Signal Preview Window
• Add support for baseline and activation maps in Live Preview
• Add menu to easily modify devices and tools

See the open issues for a full list of proposed features (and known issues).

(back to top)

License

Distributed under the MIT License. See LICENSE.txt for more information.

(back to top)

Contact

Created by Maxence Pelletier-Lebrun - [email protected]

For a research internship at Michèle Desjardins' Laboratory

Research Page: https://www.crchudequebec.ulaval.ca/recherche/chercheurs/michele-desjardins/

Project Page: https://github.com/midesjardins/Widefield-Imaging-Acquisition

(back to top)

Acknowledgments

This project was made possible with the help of these open-source ressources:

• Tabler Icons
• Pylablib
• Best-README-Template

(back to top)

widefield-imaging-acquisition's Issues

save np arrays periodically

create separate vectors when separating files

implement different signal shapes?

matplotlib resets wrong plot after roi is set

verify with daq that signal is good width

Baseline not saving in text file when in root

ROI something freezes

add baseline stimulation type

Add option to start without any lights (two-photons)

Improve Numpy Performance

check if file already exists and ask if user wants to override it

Activate all buttons when run completed

improve efficiency of signal generation

Fix Signal Preview freezing

add option to import json configuration file

Verify channel ordrer in preview

Test issue

Add progress line in signal preview

verify that matplotlib preview works at high frequencies

Stim not saved in vectors, everything false in lights / cam except first item

fix non square imports in scout

create parent software to separate arrays

Impossible to reset ROI under certain conditions

Make matplotlib plot generation in thread?

Sample stime at 3000

Test issue 2

Add option for trigger start

icons do not always show on widefield computer

add stimulation channel for co2 pump

set a 57 fps limit on framerate

ask to delete files if experiment is stopped

add menu to modify instrument ports

Change colors when superimposing signals

add option for binning

always run root when experiment is run

remove heigth and signal types from co2 channel

Save numpy arrays in append mode

Add option to change signal height for analog outputs

fix support for floats on widefield computer

implement channels for scout

Update readme

option to change height of analog stimulations

shrink_array does not set correct extents

Clean Up Code Artifacts and Split Interface (2022-07-11)

Not all channels show (only green)

Verify ROI Dimensions

close all lights at startup

Extend light duration beyond camera exposition

check for existing files in webcam

Add slider to ajust sensibility