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Stand With Ukraine

Selective Plane Illumination Microscopy Setup

Fluorescence Imaging Laboratory, Kyiv, Ukraine

__L-SPIM v0__

L-SPIM v0 parameters overview

Parameter Value
Detection objective Olympus PlaN 10x 0.25
Magnification 5.56x
Camera Basler Ace 2R Pro (a2A5320-23umPRO), 5320x3032 px (16.1 Mpx)
Pixel size 0.493 μm/px
Field of view 2.62x1.49 mm
Z-stack step resolution 16 μstep/μm (0.0625 μm/μstep)
Lateral resolution, FWHM theoretical/estimated 1.12 μm/2.06 μm
Axial resolution, FWHM theoretical/estimated 11.70 μm/ 6.32 μm
Excitation lasers 510 nm, 640 nm
Emission filters Chroma HQ545/40m, Chroma D620/20m

Detection arm

Detection params

Parameter Value
Detection objective Olympus PlaN 10x 0.25 FN 22 (F18)
Detection tube lens F100
Magnification ~5.56x
Camera Basler Ace 2R Pro (a2A5320-23umPRO)
Pixel size 0.493 μm/px
Field of view 2.62x1.49 mm
Theoretical resolution (500 nm) 1.220 μm
Theoretical depth of field (500 nm, n=1.33) 10.640 μm
Z-stack step (Sutter Instruments MPC-200 with MP225/M) 0.0625 μm/μstep (16 μstep/μm)

Filters

Excitation arm

Light path

Lasers

Control software

Micromanager configuration

Camera

Model Basler Ace 2R
ID a2A5320-23umPRO
Sensor Sony IMX542 (CMOS)
Sensor size 14.58x8.31 mm (1.1")
Sensor diagonal 16.78 mm
Pixels (HxV) 5320x3032 (16.1 Mpx)
Pixel size 2.74x2.74 μm
Frame rate up to 24 fps

GPIO pinout

Pin Function I/O Line Colour
1 12–24 VDC camera power - Brown
2 Opto-coupled I/O input line Line 1 White
3 Ground for opto-coupled I/O line - Blue
4 General purpose I/O (GPIO) line Line 2 Black
5 General purpose I/O (GPIO) line Line 3 Grey
6 Ground for camera power and General Purpose I/O (GPIO) lines - Pink

Basler Power-I/O Cable

GPIO configuration

Pylon Viewer v7.2 camera parameters, category Digital I/O Control:

  • Line Selector: Line 2
  • Line Inverter: not selected
  • Line Mode: Output
  • Line Source: Acquisition Active

Sync

Synchronisation with Arduino32bitBoards, specs for ESP32:

  • Baudrate: 115200
  • Laser TTL trigger module requires 5V, need level conversion 3.3V -> 5V

Pinout:

  • Trigger: Pin 5 - camera Line 2 input
  • Channel 1: Pin 25/DAC - Level Converter ON
  • Channel 2: Pin 26/DAC - 510 nm trigger
  • Channel 3: Pin 27/PWM - 640 nm trigger
  • Channel 4: Pin 15/PWM
  • Channel 5: Pin 14/PWM
  • Channel 6: Pin 4/PWM
  • Channel 7: Pin 23/PWM
  • Channel 8: Pin 19/PWM

Switch states

Laser Pin Hight State
510 nm 25+26 (Ch.1+Ch.2) 3
640 nm 25+27 (Ch.1+Ch.3) 4 (not working)
510 nm + 640 nm 25+26+27 (Ch.1+Ch.2+Ch.3) 6 (not working)

Hardware config

License

This open-source project is released under the CERN Open Hardware License. Our aims are to promote open scientific hardware development and to share our engineering solutions.

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SPIM-based setup for whole-organs volumetric imaging

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