Welcome to…¶
Wide-Field Optical Mapping (but Python)¶
About WFOM¶
Wide-Field Optical Mapping (WFOM) is the product of the Columbia University’s Laboratory for Functional Optical Imaging, run by Elizabeth Hillman
Technique¶
WFOM works by utilizing a high-speed CCD camera’s exposure signal to trigger arrays of high-powered LEDs, set to specified wavelengths.
A paper describing the technique further can be found here.
Applications¶
WFOM is currently being used in a wide (•͡˘㇁•͡˘) range of applications, such as:
Neurovascular Coupling¶
Seizure caused by tumor growth imaged using WFOM¶
Resting State Dynamics¶
Resting state neural and hemodynamic activity in the awake mouse brain¶
For a comprehensive list of WFOM applications, visit this page
Why PyWFOM?¶
PyWFOM combines code previously spread across numerous platforms, devices,
and languages into a single, user-friendly Python Package.
Users are able to set camera parameters, stim functions, and data acquisition all in one place.
Create Virtual Machine¶
It is highly recommended you use a Virtual Environment when installing
pywfom. This is done by running the following commands:
python3 -m venv myWFOM
source myWFOM/bin/activate
Installing PyWFOM¶
System Requirements¶
Windows 10 or Linux
Python 3.5+
Arduino Setup¶
Running pywfom requires first setting up an Arduino
to be used with the system.
Installing the Arduino IDE & Drivers¶
Download the Arduino IDE for your Operating System and follow the instructions on your screen.
Any required USB Drivers will be installed alongside the Arduino IDE.
Deploying to the Arduino¶
Attach the Arduino you wish to use with your
pywfomsystem to your machine via USB.
NOTE: Arduino MEGA is suggested
Download the pyWFOM Arduino File
Start the Arduino IDE, and open the pyWFOM Arduino File
Verify the correct device and port are selected
These can be changed from the Tools Menu¶
Deploy the code to the Arduino
Wait until the code successfully deploys¶
pywfomis now able to send settings to your Arduino
Attaching Devices¶
Adding devices to your pywfom system is as simple as attaching them
to the pins of your Arduino.
The example below shows 3 separate BNC connectors attached to an exposure trigger from a sCMOS camera and two LED drivers.
Simple wiring diagram including a single sCMOS Camera and 2 LEDs¶
pywfom would send this information to the Arduino using the
strobing setting in config.json.
Take a look at the section on the JSON Configuration File.
{
"strobing": {
"leds":[
{
"name":"led1",
"pin":2
},
{
"name":"led2",
"pin":5
}
],
"trigger":11
]
}
Quickstart¶
Once you’ve completed Installing PyWFOM and Arduino Setup, the system can start to be configured.
The quickest way to do this is running the wfom-quickstart command.
wfom-quickstart
Command Line Tools¶
The simplest way to configure, acquire, and view runs is with one of pywfom’s
available Command Line Tools.
Command |
Description |
|---|---|
Creates a System Interface and opens the Main Frame |
|
View Acquisition Files in the Run Viewer |
|
Quickly start an acquisition using the default settings |
wfom¶
Arguments¶
Argument |
Name |
Description |
|---|---|---|
-v |
–verbose |
Determines whether pyWFOM prints to the console |
-t |
–test |
Runs pyWFOM in ‘Test Mode’ |
-c |
–config |
Include a string for the location of a JSON Config File |
-s |
–solis |
Runs pyWFOM in ‘Solis Mode’ |
wfom -v -c path/to/config/myConfiguration.json
wfom-viewer¶
wfom-quickstart¶
Acquisition Files¶
Raw Data is stored as a individual frames in a run directory. frame
file are numpy array, and saved as an npz file with the following structure.
Structure¶
run12
├── config.json
├── frame0.npz
│ ├── cam0
| | └── array
│ ├── cam0
| | └── array
│ └──arduino
| └── message
├── frame1.npz
.
.
.
└── frameN.npz
Numpy Frame¶
JSON Configuration File¶
pywfom uses a JSON file to store various metadata and settings.
Setting |
Description |
Type |
Example |
|---|---|---|---|
user |
Name or ID of individual who ran the acquisition. |
string |
“rjb2202” |
mouse |
Name or ID of the mouse the acquisition was conducted on. |
string |
“cm100” |
directory |
Location data will be saved to |
string |
“C:/data” |
runs |
Number of runs for given acquisition |
int |
5 |
run_length |
Length of each acquisition (in seconds) |
float |
10.0 |
cameras |
List of camera settings |
list |
See Cameras |
arduino |
Dictionary of arduino settings |
dict |
See Arduino |
NOTE: It is highly recommended you only alter the your JSON Configuration File , do not directly edit the file itself.
Example JSON Configuration¶
{
"user":"rjb2202",
"mouse":"cm100",
"directory":"C:/data",
"runs": 5,
"run_length": 2.0
"arduino": {}
"cameras": []
}
Arduino¶
{
"arduino": {
"port": "COM4",
"data_acquisition":[
{
"name":"encoder",
"pin":20
}
],
"strobing": {
"leds":[
{
"name":"blue",
"pin":7
},
{
"name":"green",
"pin":8
}
],
"trigger":2
},
"stim": [
{
"name":"default",
"type":"2PinStepper",
"pins":{
"step":5,
"dim":6
},
"pre_stim":4.0,
"stim":7.0,
"post_stim":8.0
}
]
}
}
Cameras¶
{
"cameras": [{
"device": "test",
"index": 0,
"name": "cam1",
"height": 564,
"width": 420,
"offset_x": 524,
"offset_y": 157,
"binning": "1x1",
"dtype": "uint16",
"master": true,
"framerate": 20.0
}, {
"device": "test",
"index": 0,
"name": "cam3",
"height": 500,
"width": 400,
"offset_x": 1,
"offset_y": 50,
"binning": "1x1",
"dtype": "uint16",
"master": false,
"framerate": 10.0
}]
}