SPIMvi!

Schemes

Plugin

Briefly, we use three different laser sources L (MBL, Obis Coherent, and Omicron), one for each wavelength 473 nm, 561 nm and 638 nm, respectively. The laser intensity is controlled via software for 561/638 nm and for 473 nm we used an automated varying neutral density filter. Then we combine them using a combination of silver mirrors (Thorlabs PF10-03-P01) and dichroic mirrors (Thorlabs DMLP605R and DMLP505R).

After all aligned, the laser is split in a 50/50 beam splitter (Thorlabs CCM1-BS013/M), in order to obtain two symmetric illumination paths. The laser scanning is carried in the vertical axis using a galvanometric mirror GM1/GM2 (Thorlabs GVS201) which optical plane is conjugated with the back focal aperture of an objective lens (Nikon Plan Fluor 10× 0.3 WD16.0 mm) using a 4.0× telescope system consisting in a 100 mm and a 400 mm plano-convex lenses. Right before the back focal aperture, we have an iris diaphragm (Thorlabs SM1D25) to change the numerical aperture.

For detection, we place a dry objective (Nikon Plan Fluor 4× 0.13NA WD17.4 mm or Nikon Plan Fluor 10× 0.3NA WD16 mm) or an immersion objective (Nikon LWD 16× 0.8NA WD 3 mm), perpendicular to the excitation plane, to collect the fluorescent emission. To prevent any excitation light to be acquired we use emission filters placed at the infinity space before the camera, mounted on an automatic filter wheel FW2 controlled by the Arduino Mega board (520/90, 600/70, 700/75, Db). Finally, a 180 mm tube lens creates the image on the chip of a CMOS camera (CAM - Hamamatsu Orca-Flash4) recording the entire illuminated plane at the same time. With the 16× objective, the total field of view is of 819.2 × 819.2 μm with a final pixel size of 0.4 μm.

The new plugin presents new features:

- Control of two pair of galvo (XY) for double side illumination.

- Direct control of XYZ stages and sample rotation. 

- Multipositioning acquisition.

- Supports confocal slit detection.

Files and installation

At the bottom of this page you would find all the files you need to run OpenSpi!n. Be aware that the download arrow is at the right side (please use scroll bar).

The system has been tested and compiled for Micromanager overnight version 1.4.23 (MMSetup_64bit_1.4.23_20170828.exe)

http://valelab.ucsf.edu/~MM/nightlyBuilds/1.4/Windows/

The content of the files is as follow:

ThorlabsKinesisBenchtop.zip: Source code for the device adapter for linear benchtop stage controller Thorlabs (C++)

ThorlabsKinesisKCubeServo.zip: Source code for the device adapter for linear KCube stage controller Thorlabs (C++)

ThorlabsKinesisTCubeServo.zip: Source code for the device adapter for linear TCube stage controller Thorlabs (C++)

Control_OpenSpi!n.zip: Source code of the Micromanager plugin (Java).

x64.zip: Compiled version for 64 bits. 

For installation:

1.  Uncompress x64.zip

2.  Control_OpenSpi!n.jar and Config_EX_file.txt should be copy/pasted onto the mmplugin folder.

3. The rest of files (device adapters) should be copy/pasted on the main Micromanager folder.