IGC

OPenT | Reservations

  • OpenT

  • OPenT (Optical Projection Tomography).

    Location : UIC Room 6 (0B07), Bartolomeu Dias wing

    Microscope: Custom made body

    Year Installed: 2014

    Camera: Hamamatsu Flash Orca 4.0 LT 2048*2048*

    Optics: Fluorescence and Transmitted light

    Operating: BABB or other clearing protocols2)

    * - camera may be working at a lower format.

    Keywords: OPT, Tomography, clearing, large samples


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Suggestion for description in "Materials and Methods":

Sample material and methods text under construction.

Suggestion for "Acknowledgments":

We would like to thank the technical support of IGC's Advanced Imaging Facility (AIF-UIC), which is supported by the national Portuguese funding ref# PPBI-POCI-01-0145-FEDER-022122, co-financed by Lisboa Regional Operational Programme (Lisboa 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER) and Fundação para a Ciência e a Tecnologia (FCT; Portugal).

Maintenance log:

Booking Calendar details

Configuration
Value
Booking type
Pre-reservation with admin confirmation
Responsible
Gabriel Martins
Minimum booking time (in min)
60
Schedule tolerance (in days)
14
Detele tolerance (in hours)
0
Booking restriction status
Disabled

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.

Place mouse over Magnification to see the objective.
Magnification
Objective type
NA1
Immersion
Working distance (mm)
Resolution2 @525nm in XY
Image Pixel size3
Image Pixel size SIM3
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 are estimates. 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.

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
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  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)