View source for Setup Extensions and Modifications

= 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: [http://george.ph.utexas.edu/~meyrath/informal/shutter.pdf paper by Todd P. Meyrath] and [https://micro-manager.org/wiki/Control_laser_shutters_with_Arduino 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):

#Download the micro-manager source code as instructed here (https://micro-manager.org/wiki/Micro-Manager_Source_Code).
#Instal all the relevant programs for building micro-manager as instructed here (https://micro-manager.org/wiki/Building_MM_on_Windows).
#Setup up Visual C++ 2010 Express as here (https://micro-manager.org/wiki/Visual_Studio_project_settings_for_device_adapters).
#Instal the 64bit APT software from Thorlabs (https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=Motion_Control&viewtab=1).
#Download and unzip the APTx64 form here (https://micro-manager.org/wiki/File:APT_x64.zip).
#Then build the ThorlabsAPTStage Device Adapter in 64bit on a 64bit Windows 7 machine, using the 'APT.lib' downloaded in point 5.
#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 point 5.
#The OpenSPIM Fiji/MM bundle can then restarted and a ThorlabAPTStage could be configured as described for a 32bit system here (https://micro-manager.org/wiki/ThorlabsAPTStage).

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).


{| class="wikitable sortable" border="1"
|-
! scope="col" class="unsortable" width="100"| Manufacturer
! scope="col" class="unsortable" width="150"| Accessibility 
! scope="col" class="unsortable" width="250"| Description
! scope="col" class="unsortable" width="130"| File or Link/Model #
! scope="col" class="unsortable" width="125"| Image
! scope="col" class="unsortable" width="50"| Quantity
! scope="col" class="unsortable" width="50"| Price (EUR)
|- align="center"
|| Nikon
|bgcolor="pink"| purchase  
|| 4X Nikon Plan Fluorite Imaging Objective, 0.13 NA, 17.2 mm WD, dry
|| [https://www.thorlabs.de/thorproduct.cfm?partnumber=N4X-PF N4X-PF] 
||[[File:Thorlabs_N4X-PF_objective.jpg|thumb|upright=0.7|center]]
|| 2 (or 3 for double illumination)
|| 410
|- align="center"
|| Thorlabs
|bgcolor="pink"| purchase  
|| Translating Lens Mount for Ø1" Optics (for the objectives
|| [https://www.thorlabs.de/thorproduct.cfm?partnumber=LM1XY/M LM1XY/M] 
||[[File:Thorlabs_LM1XY_mount.jpg|thumb|upright=0.7|center]]
|| 2 (or 3)
|| 125
|- align="center"
|| Nikon
|bgcolor="pink"| purchase  
|| Infinity-Corrected Tube Lens for Plan Fluorite Objectives 
|| [https://www.thorlabs.de/thorproduct.cfm?partnumber=ITL200 ITL200] 
||[[File:Thorlabs_ITL200_lens.jpg|thumb|upright=0.7|center]]
|| 1
|| 405
|- align="center"
|| Monika
|bgcolor="green"| self made 
|| This chamber can be 3D printed. For windows use 24x24 mm microscopy cover glasses and glue (eg. two component epoxy)
|| [https://github.com/openspim/openspim-parts/blob/master/Chambers/Dry_Objectives_Chamber_and_Holder/Chamber.stl  .stl on Github]
|| [[File:Large samples chamber 3D.PNG|thumb|upright=0.7|center]] 
|| 1 
||
|- align="center"
|| Monika
|bgcolor="green"| 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
|| [https://github.com/openspim/openspim-parts/blob/master/Chambers/Dry_Objectives_Chamber_and_Holder/Metal_Holder.pdf drawing on Github] [https://github.com/openspim/openspim-parts/blob/master/Chambers/Dry_Objectives_Chamber_and_Holder/Metal_Holder.step step file on Github]
|| [[File:holder.PNG|thumb|upright=0.4|center]] 
|| 1 
||
|}