Data Management

This page covers how the lab stores research data and how microscopy images should be prepared for internal and external presentation.

Data Storage

  • All lab data should be stored on BioHPC.

  • New users should register for an account at BioHPC account registration.

  • BioHPC access is a standard requirement for working in the lab, and new users are typically directed to an orientation or training session during setup.

  • The primary archive location for lab data is /archive.

  • Organize data routinely and remove material that no longer needs to be kept; storage has a real operational cost.

  • If data support a manuscript, preserve the raw data in a recoverable form.

  • If compression is used for archived data, it should be lossless.

Best Practices for Digital Images

Microscopy data are quantitative, and image display choices can either clarify or distort that information. Use the following practices when preparing figures, slides, or internal review materials.

Scale bars

  • Include a clearly labeled scale bar on microscopy images.

  • In Fiji, confirm the pixel size with Analyze > Set Scale before adding the scale bar.

  • Add a scale bar with Analyze > Tools > Scale Bar.

  • Flatten overlays before export if the image will be viewed outside Fiji or ImageJ.

  • Sanity-check the displayed scale against a known biological feature.

Gamma

  • Any gamma correction should be disclosed in a manuscript, slide deck, or other context where the image is presented as data.

  • Gamma correction is non-linear and can make an image unsuitable for quantitative interpretation.

  • Perform measurements on raw image data, not on gamma-adjusted exports.

Lookup tables

  • For single-channel data, grayscale is usually the clearest choice.

  • For multichannel data, prefer color combinations that remain interpretable to colorblind viewers, such as green/magenta instead of red/green.

Brightness and contrast

  • Avoid unnecessary saturation when adjusting image display settings.

  • If some saturation is unavoidable, make sure the displayed range still shows the structure that matters for interpretation.