IGC

DeltaVision OMX - SIM | Reservations

  • DeltaVision OMX

  • Deltavision OMX microscope is a Structured Illumination (SIM) super-resolution microscope based on the Deltavision core.

    Location : Bartolomeu Dias wing, UIC Room 1

    Microscope: Olympus GE DeltaVision Core

    Camera: PCO Edge 5.5 sCMOS 2560x2160*

    Optics: Fluorescence and DIC + Deconvolution

    Operating: Temperature & atmosphere control (37°C + Humidity + CO2)

    * - Camera does not work at full frame resolution, only 1024x1024 or lower to avoid field illumination problems.


  • SIM microscopy is one of the super-resolution techniques developed to overcome physical limits of resolution a normal microscope can achieve (normally about 200nm for both widefield and confocal microscopes), by applying several illumination patterns to the sample to create Moiré patterns.

    Moire Patterns with rotation

    These patterns contain high order spatial information that can later be extracted by computational algorithms using Fourier space. A typical SIM image is a reconstruction of several patterned images, where the illumination pattern changes in both angle or phase in order to extract the most out of an image. This system requires at least 15 frames per image (3 angles and 5 phases).

    SIM modulation - Reconstruction > SIM reconstruction

Suggestion for description in "Materials and Methods":

Images were acquired on an GE HealthCare Deltavision OMX system, equiped with 2 PCO Edge 5.5 sCMOS cameras, using the a 60x 1.42NA Oil immersion objetive, GFP + CY5 fluorescence filtersets and DIC optics. Images were deconvolved/reconstructed with Applied Precision's softWorx software.

Maintenance log:


Laser Unit

Laser
Excitation lines
Maximum power
405
405 nm
100 mW
488
488 nm
100 mW
568
568 nm
100 mW
640
640 nm
100 mW

Available objectives

Below is a list of the objectives and filters available. On the DeltaVision system, the filter cube (dichroic) is manually set and the emission filters are split between two filter wheels that also need to be manually switched. Make sure that both match the excitation and emission filters you want to use.

Move mouse over me!
Magnification
Objective type
NA1
Immersion
Working distance (mm)
Resolution2 @525nm in XY (µm)
Image Pixel size3 (µm)
Image Pixel size SIM3 (µm)
Link
20x
UPlan SAPO
0.75
-
0.60
0.427
0.240
0.120
60x
Plan Apo N
1.42
OIL
0.15
0.226
0.080
0.040

(1) NA - Numerical Aperture. For more information, follow this link.

(2) These values are the theoretical optical resolution limits depending on the NA of the objective and were calculated using the Resolution formula adapted to fluorescence as seen in the Olympus micro website: R = 0.61*λ/NA

(3) The pixel size saved automatically with the .dv files. The values on this table were measured with a stage graticule, with and without the 1.6x auxiliary magnification. For more accurate measurements use these values instead. Use Bio-formats to open the images in ImageJ/Fiji (already installed in the Fiji package).

IMPORTANT: For optimal deconvolution you may use the 1.6x auxiliary magnification, however, using this may cause aberration on the edges of the field of view!


Installed filtersets

Fluorescence filterset
Emission wavelength (λ)
Description
Camera
DAPI
435/31
DAPI, Hoesche, etc.
1
GFP
528/48
GFP, FITC, Alexa Fluore 488, etc.
1
RFP
609/37
RFP, TRITC, mCherry, AF568, etc.
2
Cy5
683/40
Far Red, Cy5, AF633, AF647, etc.
2
DIC
-
Transmitted Light
1/2

Spectra, lines & filters:


Setup

Turning system ON

  1. Step 1
  2. Step 2
  3. Step 3
  4. Step 4
  5. Step 5
  6. Step 6
  7. Step 7

Turning OFF

  1. Step 1
  2. Step 2
  3. Step 3
  4. Step 4
  5. Step 5
  6. Step 6
  7. Done!
  8. TAKE OUT EVERYTHING YOU BROUGHT!, eg, pipettes, slides, etc...

Getting your files

The DeltaVision tends to create large files because of the capability to perform live imaging with multiple channels and multiple positions. As such it has been setup as an FTP server so users can download the files from the comfort of their desk. Learn how to below.

  1. Install the File-Zilla Client.
  2. Quick connection, fill the top bar:

    Host:

    • Deltaivision microsocpe: dvm
    • Deltavision workstation: dvw

    username & password

    • username: igcuser
    • corresponding password
    • Port: 22
  3. After you click connect, you should get some messages on the top text window and a new file tree should appear on the right; these are your DeltaVision files.
  4. Find a folder you want to save your files to on the list on the left.
  5. To transfer files, just drag from the right to the left.
  6. Done!

If you want to learn more timesaving features of FileZilla, visit their website.


Extra Info

ImageJ/Fiji recognize and open DeltaVision .dv files, but you will need to use the Bio-Formats plugin. This plugin is available by default in the Fiji distribution.

To install the plugin in ImageJ, download the latest stable release of Bio-formats and drag it into the plugins folder. Once you start ImageJ again it will appear on the plugins menu. Go to "Plugins>Bio-formats>Bio-formats importer" or drag-and-drop a file in ImageJ/Fiji to open it.

Differential Interference Contrast (DIC)