McScope

This page is about a reference DIY microscpoe control system similar to those used by John McMaster. Its intended to be a good starting place for what options might be for adding automated image capture to a microscope.

You should also take a look at Micro-Manager. If you have a supported stage it may be a better fit

Above: high level sample architecture. In this example one axis uses an MDrive17 and a second axis uses a generic stepper motor without integrated driver. However, in a real system you probably want X and Y to use the same motor/drive

Useful links:

• https://github.com/SiliconAnalysis/pyuscope
• https://github.com/SiliconAnalysis/bbb-scope/blob/master/b3index_r1/b3index_r1/b3index_r1.pdf
• https://microwiki.org/media/scopetek/0001-scopetek-directly-control-RGB-gain.patch
• https://microwiki.org/wiki/index.php/Stepper_Motor
• https://www.machinekit.io
• https://beagleboard.org/black

Terminology:

• Indexer: a device that generates step/direction pulses
• Drive: power electronics for (stepper) motor
• Beaglebone Black (BBB): embedded board with lots of accurate timing I/O
• Machinekit: a CNC controller (indexer) distribution for BBB. Based on LinuxCNC
• BBB Indexer (B3I) cape (PCB): allows BBB I/O to adapt to current/voltage requirements of typical drive photodiodes with convenient connections
• BBB Indexer (B3I) system: b3i PCB + BBB assembly

Reference system, focusing on critical components:

• Microscope
  • AmScope MU800 camera
  • MDrive17 stepper motors on XY stage
• b3i system
  • BBB
  • Machinekit
  • B3I cape
• T61p laptop
  • Ubuntu 16.04LTS
  • pyuscope (microscope control software)
  • touptek.ko modified for direct RGB control

Misc notes:

• b3i default configuration is to power I/O buffers from "SYS_5V", which means external power is required. The easiest way to do this is to supply 5V to the barrel jack using a second USB to barrel jack cable

machinekit setup

Start by ssh-copy-id to your BBB to ease future operations. You may also want to setup /etc/hosts entry:

192.168.7.2 mk

And ~/.ssh/config:

 Host mk
 HostName mk
 User machinekit
 StrictHostKeyChecking no

Then prepare a config based on an unscaled template:

cp -r config/scale1_b3i/ config/my_config/

If you know how many steps per mm, edit my_config/axis.ini to set SCALE. For example, if you have:

• 1.8 degree / step motor
• 16 pulse / step microstepping
• 2 rev / mm

You will need to set SCALE to 360/1.8 * 16 * 2 = 6400. In any case, after you edit SCALE, launch the GUI and try moving against a known size object and see if it looks about right. You may want to also just other parameters like MAX_VELOCITY and MAX_ACCELERATION. Its easiest to copy repo to BBB using scp. Consider adding a script to the BBB named run.sh like:

linuxcnc pyuscope/config/my_config/axis.ini

pyuscope setup

Ubuntu 16.04

cd ~
git clone https://github.com/SiliconAnalysis/pyuscope.git
cd pyuscope
sudo apt-get install -y python-qt4 python-gst0.10 python-paramiko python-serial
sudo pip install pillow

Once software is setup, start setting up a microscope on your host:

cd ~/pyuscope
cp config/test/microscope.json config/my_config/
ln -s config/my_config/microscope.json .

Edit microscope.json and set x_view to reflect the field of view (in mm) for your objective(s)

Camera calibration

This is optional, but recommended for serious use. Consider getting a basic system setup first and then come back to it

Apply this patch to touptek.c and install the updated kernel module:

https://microwiki.org/media/scopetek/0001-scopetek-directly-control-RGB-gain.patch

Insert a neutral sample onto your microscope, such as a blank wafer or the back of an IC. Slightly defocus view

python util/bal_gui.py

Hit AWG repeatedly until Red Balance (R_B) and Blue Balance (B_B) have settled to near 0. Copy the values into microscope.json:imager.v4l2 entry. The top entry is default / takes priority. See config/pr0nscope/microscope.json for example. After applying open pyuscope GUI and verify the image is white balanced to gray.

pyuscope workflow

• Connect BBB over USB to host laptop
• Host laptop: static config IP to 192.168.7.1
• SSH -X from T61p to BBB (192.168.7.2)
  • Launch LinuxCNC software over X
  • Launch server.py RPC client (TODO: bring back automatic launch)
  • Use LinuxCNC GUI for all setup movement, not pyuscope
• Optional: white balance camera using cal.py. Write values to microscope.json
• Start pyuscope software
• Select current objective (ie 20x)
• Use LinuxCNC GUI to navigate around stage and make adjustments to level out
  • TODO: add link / suggestions how to do this
• Use LinuxCNC GUI to navigate to upper left corner of die and in pyuscope hit "set upper left"
• Use LinuxCNC GUI to navigate to lower right corner of die and pyuscope hit "set lower right"
• Hit run (with dry checked)
• Verify results look reasonable
• Uncheck dry
• Hit run
• Profit

Finally, note that the resulting files can be post-processed with pr0nstitch