Difference between revisions of "McScope"

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Line 39: Line 39:
 
**touptek.ko modified for direct RGB control
 
**touptek.ko modified for direct RGB control
  
−
Reference 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"
 
  
 
Misc notes:
 
Misc notes:
Line 62: Line 47:
 
===machinekit setup===
 
===machinekit setup===
  
−
cp -r config/brainscope_b3i/ config/my_config/
+
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
  
 
<br />
 
<br />
Line 75: Line 82:
 
  sudo apt-get install -y python-qt4 python-gst0.10 python-paramiko python-serial
 
  sudo apt-get install -y python-qt4 python-gst0.10 python-paramiko python-serial
 
  sudo pip install pillow
 
  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)
 +
 +
 +
===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

Revision as of 08:29, 19 August 2019

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.

Mcscope overview thumb.png


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:

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)


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

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