Barresi Lab Capstone Group

Team Members:

• Summer Yu
• Haley Schmidt
• Carol Milton
• Catherine Kung

Installations Necessary for Python Plugins in Imaris

The following steps have already been implemented at the Imaris Workstation.

1. Connect plugin folder to the IMARIS python path

2. Find Path created for Xtension -> download Python 3.7.12 -> download VS Code in console command

3. Download Git for windows -> Download extension for Github

Setting up Github extension for VS Code:

guideline source

1. If there is an Error Message: not find “requests” -> Solve with pip install requests

2. Genereate ssh-keygen: id_rsa(file name), barresiprojectfall2021(key)

3. Add to ssh key in Github account and clone

4. git config --global user.name to enter username

5. git config --global user.email to enter email

6. git clone

Documentation of Python XTensions for Imaris

Linking to ImarisLib

Code to link to ImarisLib:

import ImarisLib

def BLANK(aImarisId):

  # Create an ImarisLib object
  vImarisLib = ImarisLib.ImarisLib()

  # Get an imaris object with id aImarisId
  vImarisApplication = vImarisLib.GetApplication(aImarisId)

  # Get the factory
  vFactory = vImarisApplication.GetFactory()

  # Get the currently loaded dataset
  vImage = vImarisApplication.GetDataSet()

  # Get the Surpass scene
  vSurpassScene = vImarisApplication.GetSurpassScene()

Getting User Input and Displaying Output

Use the tkinter Python library to get input from the user and display output through the GUI (Graphical User Interface).

global Entry1

def dialog(): ## If you want to do so converting at the initial entry
    global Entry1, vChange
    vChanged=Entry1.get()
    vChange=float(vChange)

root=Tk()
root.geometry("200x50-0+0")
#Set input as the top level window
root.attributes("-topmost", True)
##################################################################
#Set input in center on screen
# Gets the requested values of the height and widht.
windowWidth = root.winfo_reqwidth()
windowHeight = root.winfo_reqheight()
# Gets both half the screen width/height and window width/height
positionRight = int(root.winfo_screenwidth()/2 - windowWidth/2)
positionDown = int(root.winfo_screenheight()/2 - windowHeight/2)
# Positions the window in the center of the page.
root.geometry("+{}+{}".format(positionRight, positionDown))
##################################################################

Label(root,text="Prompt for user:).grid(row=0) ##grid sets the location
Entry1=Entry(root,justify='center',width=10)
Entry1.grid(row=0, column=1)
Entry1.insert(0, 100) # set default entry as 100

# Creates Button
Single=Button(root, text="Change Intensity", bg='blue', fg='white',command=dialog) # Previously defined dialog is called here, but it doesn't necessarily have to be called
# Set button location
Single.grid(row=1, column=1)
# Call the input window for display
mainloop()

Navigating to ImarisLib Function Documentation

Open Help > Programming Interface > Data Structures > Data Fields > All

Search through functions by letter.

Integrating XTension within Imaris

In the Edit menu select Menu > Preferences > Custom Tools

In the XTension Folders field, specify the folder with the XTension file by clicking on the Add button. Once the path is established, Imaris will automatically update the list of available XTensions within that folder.

Running an XTension

Once XTension is integrated, it will automatically show up under the Image Processing tab. Click on your XTension to run it.