corbanswain / custom-multiphoton-patterning Goto Github PK

Convert image- or vector-based ''masks'' into command files that control 2-photon imaging software .

Jupyter Notebook 95.23% Python 4.55% Batchfile 0.22%

custom-multiphoton-patterning's Introduction

Custom Multi-photon Patterning

This codebase is design to take image- or vector-based ''masks'' and convert them into mask files that can be imported into 2-photon imaging software (PrairieView by Bruker) and direct the microscope system to selectively "expose" regions of a sample to laser power according to the mask.

Getting Started

The easiest way to start will be to download this code, and use Anaconda to setup a python environment. Then use a jupyter notebook to load and run the conversion code. You can do this via the following steps:

Download a release or clone this repository into a folder (e.g. .../cmp/) on your computer.
- Download the latest release here.
- Note: If you clone this repository, you will need to import the submodules via the following commands:
```
git submodule init
git submodule update
```
Download and install Anaconda (individual edition) if you do not already have it
From the anaconda prompt cd to this repository directory, then run one the following commands.
```
conda env create --prefix ./env --file env.yml 
```
If issues occur with the first method here you can try generating the enviornment from the explicit package list:
```
conda env create --prefix ./env --file .env-explicit.txt
```
Activate the anaconda enviornment by the following command
```
conda activate ./env
```
Open a jupyter notebook by entering the following command
```
jupyter lab getting_started.ipynb
```
Once in the jupyter notebook run and edit the cells to see how to use the mask generation codebase.

Todo

Add more examples of using parameters.
Add documentation to classes and functions.
Handling additional edge cases.

Done

Create example jupyter notebook.

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custom-multiphoton-patterning's Issues

Photoactivation Actions Failing in Prairie View

Issue Description

We are encountering an issue in which the "Actions" we utilize within Prairie View to import polygon data for photoactivation masks (PAMs) are no longer successfully running.

We have successfully run Actions for PAM generation in this way since 2019 on our system including on this current 5.8 version of the software. The issue began seemingly without cause (for the same Actions that were already working) on August 29, 2023 on our system.

Issue encountered on versions:
- Prairie View 5.8 (Update 2)
- Prairie View 5.5
Operating System: Windows 10 Enterprise 2016 LTSB
Prairie System ID: 4315

Steps to Recreate

Generate a script for mask data import:
1. Using a text editor (e.g. Notepad on windows) create a file with the following contents:
```
@ECHO OFF
notepad.exe %1
```
  Please note that this .bat file a toy script for debugging, we are using more complex batch scripts for our actual workflow; we recognize that it is possible to use notepad.exe directly as the script "Filename" for the action.
2. Save this file as pa_from_notepad.bat in a directory on your computer and close the file editor. Let's say we chose C:\pv-scripts\pa_from_notepad.bat as the full path at which to save the file.
3. To test this batch script:
  1. Navigate to the pv-scripts directory in your File Explorer.
  2. Double click the pa_from_notepad.bat file so that it runs.
  3. If your script creation was successful, you should see a new notepad window open along with a command prompt window. If this is not what you see you will need to stop and ensure the script definition is correct by repeating the prior steps.
  4. Close both windows.
Create an action in Prairie View:
1. Open Prairie View
2. Navigate to "Tools" > "Actions..."
3. Select the "Photoactivation" tab.
4. Click "New" to define a new action.
5. Provide the following for the action definition:
  1. Name: From-Notepad
  2. Filename: C:\pv-scripts\pa_from_notepad.bat
    use the directory that matches where you save the .bat on your file system.
  3. Arguments:
```
<outfile>
```
Use the action to upload mask data
1. Acquire a Single Scan within Prairie View by clicking "Single Scan"
2. Open the Photoactivation panel by clicking the "PA" button found at the top of the software.
3. In the Photoactivation panel click "Generate" > "From-Notepad"
4. If successful, a Notepad window should open (similar to the test from step 1.3) into which mask data can be written. However, this is where our script fails with the following error:

TimeStamp: 8/29/2023 11:28:50 AM
  Exception: The file exists.

  Exception.StackTrace:    at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
   at System.IO.Path.InternalGetTempFileName(Boolean checkHost)
   at Prairie_View.clsActionController.GeneratePAMask(Int32 Index)
   at Prairie_View.frmPhotoactivationToolbar.mnuGeneratePAMask_Click(Object sender, EventArgs e)
   at System.Windows.Forms.MenuItem.OnClick(EventArgs e)
   at System.Windows.Forms.MenuItem.MenuItemData.Execute()
   at System.Windows.Forms.Command.Invoke()
   at System.Windows.Forms.Control.WmCommand(Message& m)
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.ButtonBase.WndProc(Message& m)
   at System.Windows.Forms.Button.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
  Environment.StackTrace: at System.Environment.get_StackTrace()
  TargetSite: Void WinIOError(Int32, System.String)

Troubleshooting Steps We Have Taken So Far

Restarting the software and power-cycling the entire system has not worked.
Trying a different Paririe View version has not work (we tested the same steps on Prairie View 5.8 and 5.5).
I have created a test .bat file for debugging purposes that only displays a message:
pa_test_script.bat
```
msg "%username%" This script has started running.
```
- if this script successfully runs the following window will appear:
- However, when I define an Action that runs this script, the message window does NOT appear. Only the error message from Prairie View appears. This indicates that the issue is occurring within Prairie View PRIOR to the call of the Action script file.
In the Action definition we can replace the path to pa_from_notepad.bat with notepad or notepad.exe directly (removing any reference to a .bat batch file). We tried making this change and it did not resolve the issue.

Suggested Next Steps

Determine Location of `<outfile>`

If you have access to a working system, I would ask that you perform the issue recreation steps above through to the final step (3.iv).
Your working system should display a new Notepad window.
From that Notepad window navigate to "File" > "Save As..." and then report back to us on the file path at which the text file is located. A screenshot like the one shown below of the "Save As" window would be exactly what we need.
This screenshot is only a reference for the type of screenshot we need, it is NOT what we would expect you to see exactly.

Once we are able to determine the directory in which Prairie View is putting temp mask polygon definition files I will delete the contents of this directory on our filesystem as it is possible that this is what is leading to the "File exist" error.

Mask Data

In the case that you want to upload some test mask data, here is a test pattern which you can

Paste into a the Notepad window at step 3.4.
Save and close the Notepad window.
Prairie View will then take a moment to parse the mask data and render it over the image window.

Note: this data is designed for a 512 x 512 scan

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83787,0.36525,0.83787,0.63084,0.83596,0.63084,-1,0.83791,0.36916,0.83982,0.36916,0.83982,0.62889,0.83791,0.62889,-1,0.83986,0.37307,0.84178,0.37307,0.84178,0.62498,0.83986,0.62498,-1,0.84182,0.38088,0.84373,0.38088,0.84373,0.61717,0.84182,0.61717,-1,0.84377,0.38479,0.84568,0.38479,0.84568,0.61131,0.84377,0.61131,-1,0.84572,0.39064,0.84764,0.39064,0.84764,0.60740,0.84572,0.60740,-1,0.84768,0.40041,0.84959,0.40041,0.84959,0.59764,0.84768,0.59764,-1,0.84963,0.40627,0.85154,0.40627,0.85154,0.59373,0.84963,0.59373,-1,0.85158,0.41604,0.85350,0.41604,0.85350,0.58201,0.85158,0.58201,-1,0.85354,0.42189,0.85545,0.42189,0.85545,0.57615,0.85354,0.57615,-1,0.85549,0.42971,0.85740,0.42971,0.85740,0.56834,0.85549,0.56834,-1,0.85744,0.44729,0.85936,0.44729,0.85936,0.55076,0.85744,0.55076,-1,0.85939,0.45705,0.86131,0.45705,0.86131,0.53904,0.85939,0.53904,-1,0.86135,0.47463,0.86326,0.47463,0.86326,0.52342,0.86135,0.52342,-1

It should produce a PAM image similar to the following:

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