Microscopy Methods Reporting

    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 2048×2048.

    Confocal example – Zeiss LSM880 with Airyscan

    Cells expressing GFP and RFP were grown on 35 mm Mattek dishes. Imaging was performed using a Zeiss LSM880 confocal with a Axio Observer.Z1 microscope using ZEN 2.3 SP1 black edition acquisition software. The objective used was a Zeiss C Plan-Apochromat 63x/1.4 Oil DIC M27. GFP was imaged with a 488 nm Argon laser and emission window at 500-550 nm while RFP was imaged with a 543 nm HeNe laser with emission window at 580-630nm. The pinhole was set to Airy 1 with bidirectional imaging and a pixel dwell time of 1.92µs. A GaAsp detector was used to record the images and no averaging was performed. Live imaging was performed at 37°C and 5% CO2 with image channels captured sequentially in frame mode every 10 minutes for 2 hours. 3D Images were acquired by taking a z stack of 30 slices with 300nm spacing with a pixel size of 100nm.