Difference between revisions of "McScope"

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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.
 
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.
−
<br />
+
 
 +
You should also take a look at Micro-Manager. If you have a supported stage it may be a better fit<br />
 
[[File:Mcscope overview thumb.png|center|thumb]]
 
[[File:Mcscope overview thumb.png|center|thumb]]
  
Line 10: Line 11:
  
 
*https://github.com/SiliconAnalysis/pyuscope
 
*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/media/scopetek/0001-scopetek-directly-control-RGB-gain.patch
 
*https://microwiki.org/wiki/index.php/Stepper_Motor
 
*https://microwiki.org/wiki/index.php/Stepper_Motor
Line 15: Line 17:
 
*https://beagleboard.org/black
 
*https://beagleboard.org/black
  
−
Reference system, focusing on critical components
+
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
 
*Microscope
 
**AmScope MU800 camera
 
**AmScope MU800 camera
 
**MDrive17 stepper motors on XY stage
 
**MDrive17 stepper motors on XY stage
−
*BBB indexer
+
*b3i system
 
**BBB
 
**BBB
 
**Machinekit
 
**Machinekit
−
**B3I cape (breaks out step/direction to RJ45)
+
**B3I cape
 
*T61p laptop
 
*T61p laptop
 
**Ubuntu 16.04LTS
 
**Ubuntu 16.04LTS
Line 29: Line 40:
 
**touptek.ko modified for direct RGB control
 
**touptek.ko modified for direct RGB control
  
−
Reference workflow:
+
 
 +
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
 +
 
 +
<br />
 +
===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
 +
 
 +
To actually run machinekit, the first few "non-McMaster" users were shipped preloaded microSD cards. I used machinekit 2015-06-29, a bit old and not sure if its easy to get.
 +
 
 +
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 />
 +
 
 +
===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
 
*Connect BBB over USB to host laptop
Line 44: Line 125:
 
*Use LinuxCNC GUI to navigate to upper left corner of die and in pyuscope hit "set upper left"
 
*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"
 
*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
 +
 +
===Reference systems===
 +
{| class="wikitable"
 +
|+
 +
!Microscope
 +
!Description
 +
!Axes
 +
!Drive
 +
!Motor
 +
!Cape
 +
!Interconnect
 +
!Notes
 +
|-
 +
|pr0nscope
 +
|Metallurgical microscope
 +
|2
 +
|IMS MDrive17
 +
|IMS MDrive17
 +
|Breadboard
 +
|DB25 breakout
 +
|Should be easy to convert to DB25-RJ45 breakout, but if it ain't broke..
 +
|-
 +
|brainscope
 +
|Laser probe station
 +
|6?
 +
|XY (upper): Rorze RD-021M8
 +
XY (lower): MDrive23
  
−
<br />
+
Z (lower): OEM650?
 +
 
 +
theta?
 +
|XY (upper): Superior SloSyn NEMA 23
 +
XY (lower): MDrive23
 +
 
 +
Z (lower): NEMA 34
 +
 
 +
Z (upper): removed, was SloSyn NEMA 23
 +
 
 +
theta?
 +
|B3I-6
 +
|RJ45 breakout
 +
|Complex system
 +
Typically I only use XY upper
 +
 
 +
Z focus is done manually
 +
|-
 +
|k2scope
 +
|Confocal microscope
 +
|3
 +
|XY: Compumotor M series
 +
Z: Gecko G320
 +
|XY: Compumotor M series
 +
Z: DC servo
 +
|B3I-3
 +
|DB25-RJ45
 +
|I tried to manually do Z, but probably needs to be machine precise
 +
|-
 +
|xy-ray
 +
|X-ray panoramic
 +
|2
 +
|IMS MDrive17
 +
|IMS MDrive17
 +
|Breadboard
 +
|Breakout
 +
|Uses special planner, not pyuscope
 +
|-
 +
|biglin
 +
|Very large scanner
 +
|1
 +
|Rorze RD-021M8
 +
|NEMA23
 +
|B3I-2
 +
|RJ45 breakout
 +
|FUYU FSL40 1000 mm
 +
|}
 +
 
 +
==B3I==
 +
RJ45 pinout:
 +
{| class="wikitable"
 +
|+
 +
!Pin
 +
!Assigned
 +
!RBWB color
 +
!
 +
|-
 +
|1
 +
|STEP+
 +
|White
 +
|
 +
|-
 +
|2
 +
|STEP-
 +
|Blue
 +
|
 +
|-
 +
|3
 +
|User
 +
|
 +
|
 +
|-
 +
|4
 +
|User
 +
|
 +
|
 +
|-
 +
|5
 +
|User
 +
|
 +
|
 +
|-
 +
|6
 +
|User
 +
|
 +
|
 +
|-
 +
|7
 +
|DIR+
 +
|Red
 +
|
 +
|-
 +
|8
 +
|DIR-
 +
|Black
 +
|
 +
|}

Latest revision as of 00:53, 12 January 2020

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

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

To actually run machinekit, the first few "non-McMaster" users were shipped preloaded microSD cards. I used machinekit 2015-06-29, a bit old and not sure if its easy to get.

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

Reference systems

Microscope Description Axes Drive Motor Cape Interconnect Notes
pr0nscope Metallurgical microscope 2 IMS MDrive17 IMS MDrive17 Breadboard DB25 breakout Should be easy to convert to DB25-RJ45 breakout, but if it ain't broke..
brainscope Laser probe station 6? XY (upper): Rorze RD-021M8

XY (lower): MDrive23

Z (lower): OEM650?

theta?

XY (upper): Superior SloSyn NEMA 23

XY (lower): MDrive23

Z (lower): NEMA 34

Z (upper): removed, was SloSyn NEMA 23

theta?

B3I-6 RJ45 breakout Complex system

Typically I only use XY upper

Z focus is done manually

k2scope Confocal microscope 3 XY: Compumotor M series

Z: Gecko G320

XY: Compumotor M series

Z: DC servo

B3I-3 DB25-RJ45 I tried to manually do Z, but probably needs to be machine precise
xy-ray X-ray panoramic 2 IMS MDrive17 IMS MDrive17 Breadboard Breakout Uses special planner, not pyuscope
biglin Very large scanner 1 Rorze RD-021M8 NEMA23 B3I-2 RJ45 breakout FUYU FSL40 1000 mm

B3I

RJ45 pinout:

Pin Assigned RBWB color
1 STEP+ White
2 STEP- Blue
3 User
4 User
5 User
6 User
7 DIR+ Red
8 DIR- Black
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