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. | ||
+ | |||
+ | 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]] | ||
+ | |||
+ | |||
+ | 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: | Useful links: | ||
− | |||
− | |||
− | |||
− | |||
− | Reference system, focusing on critical components | + | *https://github.com/SiliconAnalysis/pyuscope |
− | * Microscope | + | *https://github.com/SiliconAnalysis/bbb-scope/blob/master/b3index_r1/b3index_r1/b3index_r1.pdf |
− | ** AmScope MU800 camera | + | *https://microwiki.org/media/scopetek/0001-scopetek-directly-control-RGB-gain.patch |
− | ** MDrive17 stepper motors on XY stage | + | *https://microwiki.org/wiki/index.php/Stepper_Motor |
− | * | + | *https://www.machinekit.io |
− | ** BBB | + | *https://beagleboard.org/black |
− | ** Machinekit | + | |
− | ** B3I cape | + | Terminology: |
− | * T61p laptop | + | |
− | ** Ubuntu 16.04LTS | + | *Indexer: a device that generates step/direction pulses |
− | ** pyuscope (microscope control software) | + | *Drive: power electronics for (stepper) motor |
− | ** touptek.ko modified for direct RGB control | + | *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 | ||
+ | |||
+ | <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 | ||
+ | *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=== | ||
+ | {| 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 | ||
+ | |||
+ | 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
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
Contents
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 |