The following example python code can be used to generate a virtual reference grid for the 20×20 grid spacing included in the GelMap Sample Pack. For use with correction using BigWarp, adjust image height and width to have as many boxes as are in your acquisition (+ some buffer on each side), then upscale the image in FIJI to approximately match the pixel size.

from PIL import Image, ImageDraw

 

# Set grid parameters

image_w = 200 #Image width (px)

image_h = 200 #Image height (px)

spacing = 20 #Spacing between intersections (starter pack = 20)

line_w = 8 #Line width (starter pack = 8)



def generate_grid_image(image_w, image_h, spacing, line_w):

    # Create a new image with a white background

    image = Image.new("L", (image_w, image_h), "white")

    draw = ImageDraw.Draw(image)

    # Draw horizontal lines

    for y in range(0, image_h, spacing):

        draw.line([(0, y), (image_w, y)], fill="black", width=line_w)

    # Draw vertical lines

    for x in range(0, image_w, spacing):

        draw.line([(x, 0), (x, image_h)], fill="black", width=line_w)

    return image

 

# Generate the grid image

grid_image = generate_grid_image(image_w, image_h, spacing, line_w)

 

# Save the image or display it

grid_image.save("grid_image.tif")

grid_image.show()