JohnDMcMaster / pyuscope

py-gstreamer microscope software for panorama captures using LinuxCNC

pyuscope is a collection of python based microscope utilities. In particular:

• Complete microscope applications for a few "official" configurations
• Framework for advanced users

The flagship application creates panoramic scans using:

• LinuxCNC for motion control
• ToupTek cameras (via gstreamer) to take pictures

These panoramic scans are typically chip images (ex: see http://siliconpr0n.org/)

Notable applications:

• main_gui/main.py: primary GUI
• touptek/tvl.py: for testing touptek plugin
• demo/*.py: small tech demos

Supported hardware

Supported configurations

"pr0nscope"

• Laptop: ThinkPad T430
• OS: Ubuntu 20.04
• Camera: ToupTek E3ISPM20000KPA
• Motion control: LinuxCNC via machinekit (BBB)
• Microscope: Olympus BH2 based

WIP: 3018 GRBL

• Laptop: ThinkPad T430
• OS: Ubuntu 20.04
• Camera: ToupTek E3ISPM20000KPA
• Motion control: Grbl 1.1f
• Microscope: Olympus BH2 based

Why does the laptop matter? Mostly for the screen resolution to make the GUI nice

Supported hardware

See some high level usage notes here: https://microwiki.org/wiki/index.php/McScope

Supported gstreamer image sources:

• toupcamsrc (primary)
• v4l2src
• Other sources may work but without calibration

Supported movement sources:

• linuxcnc
• Others, but they aren't well maintained

Quick start V4L2

sudo apt-get install -y python3-gst-1.0 python3-gi python3-pyqt5 python3-usb

# install for v4l2
# https://github.com/antmicro/python3-v4l2

First you might be able to try this GUI which will try to auto-detect v4l2:

python3 util/prop_gui.py

If that doesn't work or you want the full GUI, try this:

cp -r configs/v4l2_example/ config

Edit config/microscope.json and set desired width/height. You may need to use a program like "cheese" to see what the options are

python3 main_gui/main.py

Installation

To install:

sudo python3 setup.py install

Or for development:

sudo python3 setup.py develop

Setup environment before running:

export PYTHONPATH=$PYTHONPATH:$PWD
export GST_PLUGIN_PATH=~/gst-plugin-toupcam/src/.libs/:$PWD
python3 main_gui/main.py

Why?

Originally I needed to support specialized hardware and had a burning hated for Java which is used by MicroManager, the flagship FOSS microchip software. I've warmed up to Java slightly, and its possible MicroManager is a better fit for most people. However, I've been using this workflow for years now, and will probably continue to do so

Version history

0.0.0

• Works with custom motor driver board ("pr0ndexer")
• Job setup is done through our GUI
• In practice only works with MU800 camera
• Tested Ubuntu 16.04

1.0.0

• Motor contril via LinuxCNC
• Job setup is primarily done through Axis (LinuxCNC GUI)
• Tested Ubuntu 16.04

2.0.0

• gst-toupcamsrc supported
• GUI simplified
• Job setup is entirely done through Axis (LinuxCNC GUI)
• Major configuration file format changes
• python2 => python3
• gstreamer-0.10 => gstreamer-1.0
• PyQt4 => PyQT5
• Tested Ubuntu 16.04 and 20.04

2.1.0

• HDR support
• First packaged release

2.2.0

• Enforce output file naming convention

3.0.0 (WIP)

• GRBL support
• GRBL jog support
• Coordiante system defaults to lower left instead of upper left
• Move imager controls from floating window into tab
• Major API restructure
• microscope.json small changes
• planner.json major changes
• Drop obsolete "Controller" motion control API (including Axis object)
• Drop obsolete pr0ndexer motion control support
• Drop obsolete MC motion control support