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Stanford
Laboratory Department of Pathology

MIBI Tile/SED/Array Interface 2023.11.08

[+] Citation and GitHub

[+] Optical Coregistration

  1. Required Coregistration solves the matrices needed to align optical camera image x, y pixel coordinates with stage motor x, y micron coordinates.
  2. Click the button below to copy the code to the clipboard.
  3. In the MIBIcontrol interface, type Ctrl+Shift+J to open the console.
  4. Paste Ctrl+V the code into the Console and press Enter. Open the link generated in the console.
  5. [+] Not recommended Manual coregistration
    1. The automatic coregistration above infers the MIBI's optical-to-stage motor coregistration formulas. But when the MIBI's formulas are incorrect, then automatic coregistration will also be incorrect. The procedure below corrects the coregistration for this web page but not for the MIBIcontrol interface.
    2. Contact Ionpath to correct the MIBI's optical-to-stage motor coregistration and it should usually be fixed within an hour.
    3. If you insist on kludging it yourself, click the button below to copy the code to the clipboard.
    4. Paste Ctrl+V the code into the Console and press Enter. For each fiducial, center it in the SED view and store it by typing 1, 2, 3, or 4. When finished, type Escape and open the link generated in the console.
    5. Load the image file. Drag and drop onto the page or use the file input box below.
    6. Click each Optical button and click on the center of the corresponding fiducial in the image. When finished, click Use manual coregistration.
      Fiducial Micron coordinates   Optical coordinates
      Top left x y   x y
      Top right x y   x y
      Bottom left x y   x y
      Bottom right x y   x y

[−] Files

  1. Recommended Name the slide image file with the name of your run so they pair.
  2. Required Load the slide image file. Drag and drop onto this page or use the file input box below.
  3. Required Load a JSON with ≥1 FOV from the loaded slide (needed to extract the slide ID and section ID).

[+] SED Tiler

  1. Click a box in each row below and click on the optical image to select corner points for the full SED image.
    x y
    x y
  2. Click the button below to copy the SED code to the clipboard.
  3. In the MIBIcontrol interface, type Ctrl+Shift+J to open the console.
  4. Paste Ctrl+V the code into the Console and press Enter.
  5. Switch to SED Mode, set the imaging mode to QC - 300 µm, adjust the gain, and focus the image.
  6. [+] If necessary Determine the correction coefficients using the controls.
    1. Type Shift+C to generate the checkerboard image.
    2. Adjust the coefficients using the 1, 2, 3, and 4 buttons.
    3. Type S to save the checkerboard image to a PNG file. You may add characters to the beginning of the file name but the entire file name should not exceed 255 characters.
    4. Load the checkerboard image file. Drag and drop onto this page or use the file input box in the Files section above. Shift corrections should automatically load here:
      xcorrection = Δx × + Δy ×
      ycorrection = Δx × + Δy ×
    5. Enter the amount to crop from the left and right of each maximum-sized SED tile, e.g. 0.08 crops 8% from that side.
      left   right
  7. Type Shift+T to begin the tiled SED scan. Wait until complete or type Shift+/ to halt before complete.
  8. The tiled SED image should automatically be saved once generated. You may add characters to the beginning of the file name but the entire file name should not exceed 255 characters.
  9. Load the tiled SED image. Drag and drop onto this page or use the file input box in the Files section above.

[+] Label Map

  • Optional Paste below a line- and tab-separated list of labels, e.g. a TMA from Excel.

[+] Slide Options

Tiles
Shift
Z
oom
 

[+] Import

Output

No FOVs loaded