Python code samples for Micro-manager image acquisition system
Micromanager project provides broad opportunity for constructing sophisticated image acquisition protocols (e.g. in microscopy). So it becomes possible to overreach vendor software limitation and realize your inherent researcher's freedom as far as possible.
Unfortunately, micromanager documentation lacks for detailed examples. It is not easy to understand the hardware capabilities and API logic. I hope those samples will be helpful in your journey, especially for live video acquisition.
- Getting list of available properties and their allowed values
- Video grabbing with opencv highgui
- Efficient frame conversion with Numpy (rgb32 to rgb, bgr)
- Qt GUI (property browser)
- OpenGL context for efficient video output
Install Micromanager from official website and add C:\Program Files\Micro-Manager-1.4 to PYTHONPATH system variable. After that you can simple import micromanager's core:
import MMCorePy
I made Archlinux PKGBUILD.
See test snippet at the end of the PKGBUILD.
2014-02-11T14:36:41.328125 p:612 t:2300 [LOG] Error occurred. Device BaumerOptronic. Failed to initialize circular buffer - memory requirements not adequate.
Traceback (most recent call last):[Decode error - output not utf-8]
mmc.startContinuousSequenceAcquisition(1)
File "C:\Program Files\Micro-Manager-1.4\MMCorePy.py", line 4956, in startContinuousSequenceAcquisition
return _MMCorePy.CMMCore_startContinuousSequenceAcquisition(self, *args)
MMCorePy.CMMError: Failed to initialize circular buffer - memory requirements not adequate.
Solution: Just increase circular buffer size (60 megabytes works fine for me). According with mailing list 600-800-1200 MB for circular buffer is normal.
mmc.setCircularBufferMemoryFootprint(60)
mmc.popNextImage() and mmc.getLastImage() both raises an exception while circular buffer is empty.
Solution: Check buffer for image count.
if mmc.getRemainingImageCount() > 0:
rgb32 = mmc.popNextImage()
def rgb32asrgb(rgb32):
"""View RGB32 as RGB array (no copy, very fast).
low memory address ----> high memory address
| pixel | pixel | pixel | pixel | pixel | pixel |...
|-------|-------|-------|-------|-------|-------|...
|B|G|R|A|B|G|R|A|B|G|R|A|B|G|R|A|B|G|R|A|B|G|R|A|...
http://avisynth.nl/index.php/RGB32
"""
return rgb32.view(dtype=np.uint8).reshape(
rgb32.shape[0], rgb32.shape[1], 4)[...,2::-1]
- Micro-Manager python library
- Immunopy - an Micro-manager based application (python image processing with Qt, OpenCV, OpenGL, OpenCL)