Microscopy

    Widefield is fundamentally any technique in which the entire specimen of interest is exposed to the light source, with the resulting image being viewed either by the observer or a camera.

    Confocal offers controllable depth of field, elimination of out-of-focus information, and the ability to collect optical sections from thick specimens.

    Super resolution improves resolution beyond the diffraction limit. Each method has a unique set of principles to achieve this.

    Light-sheet allows rapid 3D and live imaging of large specimens using a unique planar illumination approach while minimizing photobleaching and phototoxicity.

    Stereo microscopy allows low magnification observation of a sample to study the surfaces of solid specimens or to carry out close work such as dissection or microsurgery.

    Location: BioCity A, 5th floor, office side.

    Software:
    • FIJI
    • Ilastik
    • FlowJo V10
    • Slidebook reader
    • NIS Elements 5.02
    • Icy
    • Mathlab 2020a
    CPU: Intel(R) Xeon(R) CPU E5-1650 v4 @ 3.60GHz (6 Cores & 12 Threads)
    • Memory: 16GB RAM
    GPU:
    NVIDIA Quadro M4000
    • Display Memory: 16057 MB
    • Dedicated Memory: 8192 MB
    Reservation System: Image Analysis PC 1
    Software:
    • FIJI
    • Ilastik
    • FlowJo V10
    • Bitplane Imaris 8.1.2
    • Slidebook 6 reader
    • AutoQuant X3
    • BioImageXD
    • NIS Elements
    CPU: Intel(R) Xeon(R) CPU X5650 @ 2.67GHz (6 Cores & 12 Threads)
    • Memory: 24GB RAM
    GPU: AMD FirePro V5800
    • Display Memory: 4GB
    • Dedicated Memory: 1GB
    Reservation System: Image Analysis PC 2
    Software:
    • FIJI
    • Ilastik
    • FlowJo V10
    • Bitplane Imaris 8.1.2 full version
    • Slidebook 6
    • AutoQuant X3
    • BioImageXD
    • NIS Elements
    CPU: Intel(R) Xeon(R) CPU E5-2667 v2 @ 3.30GHz (8 Cores & 16 Threads)
    • Memory: 131GB RAM
    GPU: AMD FirePro W9100
    • Display Memory: 4GB
    • Dedicated Memory: 3GB
    Reservation System: Image Analysis PC 3
    • Huygens Essential
    • Arivis Vision4D 3.4

    Here is a visual guide that will help you track your microscopy method reporting. We also provide a general template followed by two specific examples of widefield and confocal imaging. You will find instrument-specific information on our webpages but we also suggest contacting our staff to assist with your method writing.

    Please also remember to acknowledge our core facility and Biocenter Finland.

    Acknowledgements example: Imaging/Flow cytometry was performed at the Cell Imaging and Cytometry Core, Turku Bioscience Centre, Turku, Finland, with the support of Biocenter Finland.

    General Methods Template

    Cells were [SAMPLE INFORMATION]. Imaging was performed using a [1. Microscope MAKE & MODEL]. The objective used was a [2. OBJECTIVE]. Live imaging was performed at [LIVE IMAGING]. Samples were imaged with [3. LIGHT SOURCE] with [4. FLUORESCENCE FILTERS]. Images were acquired [5. STAGE and 3D Capture] using a [6. CAMERA].

    Widefield example - Nikon Eclipse Ti2-E

    Cells were grown (fluorophores?) on No. 1.5 coverslips, fixed with 4% PFA and mounted on slides using Prolong Gold. Imaging was performed using a Nikon Eclipse Ti2-E widefield inverted microscope using Nikon NIS Elements 4.11 acquisition software. The objective used was a Nikon 63x Plan Apochromat 1.4 NA with Nikon oil immersion 1.518. Live imaging was performed with Okolab bold line heating system at 37°C, 20% O2 and 5% CO2 with images captured every 10 minutes for 24 hours. Samples were imaged with 475/28nm and 575/25nm excitation filters and 525/50nm and 600/30nm emission filters (Chroma). Images were acquired by taking a z stack of 30 slices with 300nm spacing using a Hamamatsu ORCA-Flash 4.0 v3 sCMOS camera with a pixel size of 6.5μm. Images were 16bit with pixel dimensions 2048x2048.

    Confocal example - Leica TCS SP8

    Cells expressing GFP and RFP were grown on 35 mm Mattek dishes. Imaging was performed using a Leica TCS SP8 confocal with a DMI8 microscope using LAS X 3.5.2 acquisition software. The objective used was an HC PL APO 63x/1.20 W motCORR CS2.  Samples were imaged with 488 nm and 561 nm solid-state lasers with emission windows at 500-550 nm and 580-630nm, the pinhole was set to Airy 1 and scan speed to 400 Hz. Live imaging was performed with Okolab bold line heating system at 37°C, 20% O2 and 5% CO2 with images captured every 10 minutes for 2 hours. Images were acquired by taking a z stack of 30 slices with 300nm spacing with a pixel size of 100nm.