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Setup_Extensions_and_Modifications.md

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title Setup Extensions and Modifications
layout page
description Additional setup tweaks

Bright-field illumination

Michael Redd from the Cell Imaging Core Facility at the University of Utah put together an Arduino-based solution to get proper bright-field illumination in an OpenSPIM setup: Brightfield.

Shutter

Instructions to make an Arduino-controlled shutter compatible with uManager: paper by Todd P. Meyrath and tutorial on the uManager page.

Stepper Motor Upgrade

If you would like to swap out one of the Picard stepper motors you can do so with a bit of effort.

Instructions about how to go about this for a Thorlabs DRV001 connected via a Thorlabs BSC201 controller on a 64bit OpenSPIM setup are detailed below (by Jerome Boulanger and Ben Sutcliffe):

  1. Download the micro-manager source code as instructed here.
  2. Install all the relevant programs for building micro-manager as instructed here.
  3. Setup up Visual C++ 2010 Express as here.
  4. Install the 64bit APT software from Thorlabs.
  5. Download and unzip the APTx64 form here.
  6. Then build the ThorlabsAPTStage Device Adapter in 64bit on a 64bit Windows 7 machine, using the 'APT.lib' downloaded in point 5.
  7. Rename the resulting .dll file to 'mmgr_dal_ThorlabAPTStage.dll' then place it into the OpenSPIM.app folder along with the 'APT.dll' downloaded in 5).
  8. The OpenSPIM Fiji/MM bundle can then restarted and a ThorlabAPTStage could be configured as described for a 32bit system here.

More details to follow about incorporating this into the SPIMAcquisition plugin.

OpenSPIM for large samples

Field of view

The original OpenSPIM uses a 2X expander to enlarge the laser beam to 2 mm. For larger samples a larger field of view can be preferable. This means that you will need a larger beam to create a taller light sheet. Change the second beam expander lens to f=75 mm or 100 mm and increase the distance between lenses accordingly.

Objectives

Immersion objectives with long working distance are hard to find. However, at low NA and moderate magnification, a dry objective will also work; the higher NA, the more spherical aberrations will be present. Keep in mind that when using a dry objective in immersion, the WD will increase (approximately by a factor equal to the RI of the new medium, eg. 17 mm in air will increase to 22.6 mm in water).

Example parts list

The table below lists the parts used by the OpenSPIM for brains setup built by Monika Pawłowska (Nencki Institute of Experimental Biology, Warsaw).

Manufacturer Accessibility Description File or Link/Model # Image Quantity Price (EUR)
Nikon purchase 4X Nikon Plan Fluorite Imaging Objective, 0.13 NA, 17.2 mm WD, dry N4X-PF 2 (or 3 for double illumination) 410
Thorlabs purchase Translating Lens Mount for Ø1" Optics (for the objectives) LM1XY/M 2 or 3 125
Nikon purchase Infinity-Corrected Tube Lens for Plan Fluorite Objectives ITL200 1 405
Monika self made This chamber can be 3D printed. For windows use 24x24 mm microscopy cover glasses and glue (eg. two component epoxy) Chamber.stl 1
Monika self made This holder includes two threaded holes so it's easiest to make from metal (eg aluminum). Holder is mounted on the 4D stage arm with M6 screw. Glass slide with 1 mm thickness can be held with nylon or nylon-tipped screw Metal_Holder.pdf
Metal_Holder.step		 1