A python toolkit for fluorescence microscopy that features multi IDS uEye industrial-grade CMOS cameras and Integrated Optics laser combiner MatchBox.
Project description
microEye
A python toolkit for fluorescence microscopy that features IDS uEye industrial-grade CMOS cameras.
The Acquisition Module allows multi-cam image acquisition within one graphical user interface.
The Control Module allows setting the laser excitation presets, manual focus and automatic focus stabilization by monitoring the peak position of a totally internally reflected IR beam and moving the piezo stage accordingly.
The Tiff Viewer Module allows accessing tiff images (single file and sequecnces) of order TYX (2D SMLM), also allows for visualizing the filtering-localization process WYSIWYG.
This toolkit is compatible with the hardware we are using in our microscope. For further details check our microscope's github (TBA)
Uses Packages
- Numpy
- scipy
- pandas
- Zarr
- dask
- pyueye
- cv2
- tifffile
- PyQt5
- pyqtgraph
- qdarkstyle
- ome-types
- lmfit
- pyqode.python (Jedi Fix)
- VimbaPython (Included in Vimba SDK and installed manually)
How to Install Package
> pip install microEye
Microscope Scheme
Hardware
- Supported Cameras:
- IDS uEye industrial-grade CMOS cameras, specifically UI-3060CP Rev. 2.
- Thorlabs DCx cameras using the UC480 driver, specifically DCC1545M.
- Allied Vision cameras using Vimba SDK, specifically Alvium 1800 U-158m.
- Integrated Optics Multi-wavelength Laser Combiner MatchBox.
- Piezo Concept nanopositioner for microscope objectives FOC.
- Parallax Linescan Camera Module used for IR autofocus stabilization tracking TSL1401-DB (#28317) acquisition done by an Arduino LineScanner.
- RelayBox arduino for laser control using the camera flash signal with different presets.
- Parts list related to our iteration of hohlbeinlab miCube (TBA).
Acquisition Module
How to use
from microEye.hardware import acquisition_module
try:
app, window = acquisition_module.StartGUI()
app.exec_()
except Exception as e:
traceback.print_exc()
finally:
# dispose camera adapters
for cam in window.ids_cams:
cam.dispose()
# Destroys the OpenCv windows
cv2.destroyAllWindows()
For Vimba SDK to work the script should be executed as administrator on Windows and wrapped in a with statement:
from microEye.hardware import acquisition_module
try:
import vimba as vb
except Exception:
vb = None
with vb.Vimba.get_instance() as vimba:
app, window = acquisition_module.StartGUI()
app.exec_()
Control Module
How to use
from microEye.hardware import control_module
app, window = control_module.StartGUI()
app.exec_()
Data Viewer / Processor
How to use
from microEye import tiff_viewer
app, window = tiff_viewer.StartGUI('D:/')
app.exec_()
Authors
Mohammad Nour Alsamsam
People Involved
Dr. Marijonas Tutkus (supervision)
Aurimas Kopūstas (sample preparation and experiments)
Acknowledgement
Project details
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