Using OpenCV with Tkinter

Try this code:

from PIL import Image, ImageTk
import Tkinter as tk
import argparse
import datetime
import cv2
import os

class Application:
    def __init__(self, output_path = "./"):
        """ Initialize application which uses OpenCV + Tkinter. It displays
            a video stream in a Tkinter window and stores current snapshot on disk """
        self.vs = cv2.VideoCapture(0) # capture video frames, 0 is your default video camera
        self.output_path = output_path  # store output path
        self.current_image = None  # current image from the camera

        self.root = tk.Tk()  # initialize root window
        self.root.title("PyImageSearch PhotoBooth")  # set window title
        # self.destructor function gets fired when the window is closed
        self.root.protocol('WM_DELETE_WINDOW', self.destructor)

        self.panel = tk.Label(self.root)  # initialize image panel
        self.panel.pack(padx=10, pady=10)

        # create a button, that when pressed, will take the current frame and save it to file
        btn = tk.Button(self.root, text="Snapshot!", command=self.take_snapshot)
        btn.pack(fill="both", expand=True, padx=10, pady=10)

        # start a self.video_loop that constantly pools the video sensor
        # for the most recently read frame
        self.video_loop()

    def video_loop(self):
        """ Get frame from the video stream and show it in Tkinter """
        ok, frame = self.vs.read()  # read frame from video stream
        if ok:  # frame captured without any errors
            cv2image = cv2.cvtColor(frame, cv2.COLOR_BGR2RGBA)  # convert colors from BGR to RGBA
            self.current_image = Image.fromarray(cv2image)  # convert image for PIL
            imgtk = ImageTk.PhotoImage(image=self.current_image)  # convert image for tkinter
            self.panel.imgtk = imgtk  # anchor imgtk so it does not be deleted by garbage-collector
            self.panel.config(image=imgtk)  # show the image
        self.root.after(30, self.video_loop)  # call the same function after 30 milliseconds

    def take_snapshot(self):
        """ Take snapshot and save it to the file """
        ts = datetime.datetime.now() # grab the current timestamp
        filename = "{}.jpg".format(ts.strftime("%Y-%m-%d_%H-%M-%S"))  # construct filename
        p = os.path.join(self.output_path, filename)  # construct output path
        self.current_image.save(p, "JPEG")  # save image as jpeg file
        print("[INFO] saved {}".format(filename))

    def destructor(self):
        """ Destroy the root object and release all resources """
        print("[INFO] closing...")
        self.root.destroy()
        self.vs.release()  # release web camera
        cv2.destroyAllWindows()  # it is not mandatory in this application

# construct the argument parse and parse the arguments
ap = argparse.ArgumentParser()
ap.add_argument("-o", "--output", default="./",
    help="path to output directory to store snapshots (default: current folder")
args = vars(ap.parse_args())

# start the app
print("[INFO] starting...")
pba = Application(args["output"])
pba.root.mainloop()

This should work:

import numpy as np
import cv2
import Tkinter as tk
import Image, ImageTk

#Set up GUI
window = tk.Tk()  #Makes main window
window.wm_title("Digital Microscope")
window.config(background="#FFFFFF")

#Graphics window
imageFrame = tk.Frame(window, width=600, height=500)
imageFrame.grid(row=0, column=0, padx=10, pady=2)

#Capture video frames
lmain = tk.Label(imageFrame)
lmain.grid(row=0, column=0)
cap = cv2.VideoCapture(0)
def show_frame():
    _, frame = cap.read()
    frame = cv2.flip(frame, 1)
    cv2image = cv2.cvtColor(frame, cv2.COLOR_BGR2RGBA)
    img = Image.fromarray(cv2image)
    imgtk = ImageTk.PhotoImage(image=img)
    lmain.imgtk = imgtk
    lmain.configure(image=imgtk)
    lmain.after(10, show_frame) 



#Slider window (slider controls stage position)
sliderFrame = tk.Frame(window, width=600, height=100)
sliderFrame.grid(row = 600, column=0, padx=10, pady=2)


show_frame()  #Display 2
window.mainloop()  #Starts GUI

First of all, you have the line tk.Label(imageFrame, image=show_frame()).grid(row=0, column=0, padx=10, pady=2), and since show_frame() doesn't return anything, you've set image to None. Second of all, you need to make sure you lmain.grid(), otherwise lmain won't show.

If you want to have two displays one on top of the other, you could do something like this:

import numpy as np
import cv2
import Tkinter as tk
import Image, ImageTk

#Set up GUI
window = tk.Tk()  #Makes main window
window.wm_title("Digital Microscope")
window.config(background="#FFFFFF")

#Graphics window
imageFrame = tk.Frame(window, width=600, height=500)
imageFrame.grid(row=0, column=0, padx=10, pady=2)

#Capture video frames

cap = cv2.VideoCapture(0)

def show_frame():
    _, frame = cap.read()
    frame = cv2.flip(frame, 1)
    cv2image = cv2.cvtColor(frame, cv2.COLOR_BGR2RGBA)
    img = Image.fromarray(cv2image)
    imgtk = ImageTk.PhotoImage(image=img)
    display1.imgtk = imgtk #Shows frame for display 1
    display1.configure(image=imgtk)
    display2.imgtk = imgtk #Shows frame for display 2
    display2.configure(image=imgtk)
    window.after(10, show_frame) 

display1 = tk.Label(imageFrame)
display1.grid(row=1, column=0, padx=10, pady=2)  #Display 1
display2 = tk.Label(imageFrame)
display2.grid(row=0, column=0) #Display 2

#Slider window (slider controls stage position)
sliderFrame = tk.Frame(window, width=600, height=100)
sliderFrame.grid(row = 600, column=0, padx=10, pady=2)

show_frame() #Display
window.mainloop()  #Starts GUI