Building the high-resolution, motorized OpenFlexure Microscope (v7) using the Rodeostat kit

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There were a few problems with sending commands through Python to the microscope, but it was just the outdated operating system that caused them. I wrote a quick program to stitch images together with manually entered distances to estimate the camera moving over by around a frame.

I am currently having a lot of trouble downloading the other image stitching program, and connecting the microscope to the internet.

Here are some of the outputted images

scan1.PNG
scan1.PNG1920×1440 99.7 KB

scan3scale
scan3scale1920×1440 211 KB

scan1scale
scan1scale1920×1440 106 KB

scan3.PNG
scan3.PNG1920×1440 208 KB

scan2.PNG
scan2.PNG1920×1440 99.3 KB

Here is my code because it doesn’t let me upload a .py file

import openflexure_microscope_client
m = openflexure_microscope_client.find_first_microscope()
from PIL import Image

p = m.position

x=int(input("how many frames in the x direction"))
y=int(input("how many frames in the y direction"))
focus = int(input("do you want it to autofocus every time (generally better images less precise alignment)"))

imagearray=[]
for i in range(x):
    imagearray.append([])


xframe = 3850
yframe = 2900

p["y"] -= (y+1)/2*yframe
p["x"] -= (x-1)/2*xframe
for i in range(x):
    for j in range(y):
        p['y'] += yframe
        m.move(p)
        if focus == 1:
            m.autofocus()
        im = m.capture_image()
        
        imagearray[i].append(im)
    p["y"] -= yframe*y
    p["x"] += xframe


verticalbars = []
for i in imagearray:
    images = []
    for x in i:
        images.append(x)
    widths, heights = zip(*(x.size for x in images))
    width = widths[0]
    height = heights[0]
    heightt = sum(heights)
    verticalbar = Image.new('RGB', (width, heightt))
    placeheight = (len(images)-1)*height
    for i2 in images:
        verticalbar.paste(i2, (0, placeheight))
        placeheight -= height
    verticalbars.append(verticalbar)

widths, heights = zip(*(x.size for x in verticalbars))
width = widths[0]
height = heights[0]
widtht = sum(widths)
finalimage = Image.new('RGB', (widtht, height))
placewidth = (len(verticalbars)-1)*width
for i2 in verticalbars:
        finalimage.paste(i2, (placewidth, 0))
        placewidth -= width
finalimage.show()
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