How to Report Methodology Using the micaToolbox and QCPA

The micaToolbox and QCPA framework is highly flexible, meaning there are a huge range of ways in which you can use these tools for measuring samples and testing hypotheses. In addition the type of equipment, settings and lighting used can potentially influence the measurements. The equipment and choices you make when using these tools must be clearly described in order to ensure your research is reproducible. When reporting your methods you should include:

• micaToolbox version and ImageJ version.
• Equipment; make and model of camera, lens, filter(s), underwater housing, artificial light source, background material, diffusing materials etc…
• Camera settings/strategies (e.g. ideally ISO & aperture should be kept constant, in which case state that these were kept constant and that the shutter speed was varied to control the exposure).
• Image file type/compression (RAW, JPG, etc..)
• Camera calibration (e.g. based on camera spectral sensitivities or using a chart). If you measured these sensitivities/chart reflectance values yourself then provide the raw spectral data and describe in detail how they were measured.
• Illuminant; if known, give the spectral radiance in SI units. If using an artificial light source describe the bulb type/model. If using natural light describe the conditions and how you controlled for natural variation (e.g. it would not normally be appropriate to compare one treatment which was always photographed in cloudy conditions to a different treatment in sunny conditions).
• Grey standard; specify nominal reflectance, make/model and the material of each standard. Also describe how the standard was positioned relative to the light source and sample.
• Weber fractions (also called ‘channel specific standard deviations of noise’). If these are estimated from photoreceptor abundance ratios then specify these ratios, and the Weber fraction used for the most abundant receptor type.
• Spectral sensitivities (please give the original citation, and where reconstructed from opsin curves, provide the spectral sensitivity data).
• Spatial acuity & viewing distance (please cite the original source).
• Colour & luminance discrimination thresholds.
• Relevant settings you choose in QCPA and micaToolbox (e.g. negative value replacement, etc.) The log window gives detailed information on the settings you use as you process the images.