printers and CNC machines use a text-based language known as
G-code to control their movements. In the AMi system, a
python-Tk based graphical user interface named AMiGUI controls
the movements of the plate beneath the microscope and triggers
acquisition of images of each sample. AMiGUI controls the
translation stage through G-code commands. The AMiGUI software
can be used to image an entire plate automatically, or it can
be used to look at the sample drops manually in real time.
the link for the AMiGUI.py program. To run it type “python3
you would like to take multiple images spaced in Z, you can do
so by specifying the number of images and the spacing between
them in mm. These parameters are entered in the lower right
part of the graphical user interface. When multiple z-stacked
images are collected, a command file for automatically
converting these images to a singe image with digitally
enhanced depth of field is written in the same directory. The
script requires that the program Enfuse, which is part of the
Open Source Hugin
package be installed.
can also image plates with more than one sample well at each
row/column index (i.e. a 96 well plate with three sample wells
at each of the 96 positions). See the DETAILS link for more
movement: The top part of the interface allows the plate to
be moved beneath the microscope. Movements in X and Y are
controlled by the part of the GUI that looks like a crosshair.
Clicking in the Z-translation section changes the focus.
The system needs to know the precise positions of the four
corner samples before automated imaging can commence. The TL,
TR, BL, and BL buttons move the view to the top-left,
top-right, bottom-left, and bottom-right samples, respectively.
At each position, users can make small adjustments in centering
and focus and then click SET to save the save the precise
operation: Once aligned, pushing the next and prev buttons
move from drop to drop (i.e. A11> A12> B1> B2).
Right-clicking these buttons moves up and down a row (i.e. D5 >
E5). You can also enter a position (i.e. F11) and go right
there. Left clicking the Snap Image button captures a single
image. Right clicking the button collects a Z-stack of images.
imaging: Clicking the RUN button initiates automated
imaging of the entire plate. Normally a z-stack of images is
collected at each position, and a custom command file is
written for depth of field enhancement.