Resazurin fluorescence time series, in one place
Every well from the resazurin assays in Huffmyer et al. 2026 (PeerJ 14:e21542), in one standard format. Search and plot them, then add your own experiment to see how it sits against the published studies.
Experiments
Matching wells
Rate is blank-corrected fold change per hour at the last reading. Click a column header to sort. The table shows the first 200 rows; the download has all of them.
Add your experiment
Your files are read in this browser tab only. Nothing is sent to a server. To make an experiment a permanent part of the database, download the package in step 4 and open a pull request.
Describe the experiment
experiment.json:Load the readings
sample_id, plate, type, hour, fluorescence, and temperature_c for samples. See .See it in context
Keep it
"Add to the Explorer" keeps the experiment in this browser so it shows up in Overview and Explore next time you visit. "Download submission package" saves experiment.json and readings.csv in the repository's standard layout. Put both in data/experiments/<id>/ and open a pull request; an automated check validates them and rebuilds the site.
Data format
An experiment is two files: a small description (experiment.json) and a table of plate-reader values (readings.csv). The published experiments in this site are stored in exactly this format.
Minimum required information
- About the experiment: a short id, a title, the species, a contact, the start date, and the container the animals were incubated in.
- For every well or cup: a unique
sample_id, theplate(or run) it belongs to, and whether it is asampleor ablank. - For every reading: the
hoursince resazurin was added and the rawfluorescence. - For every sample: the incubation temperature in °C.
- A reading at hour 0 for every well, and at least one later reading. Hour 0 is the baseline for fold change.
Strongly recommended: at least one blank well (resazurin solution, no animal) per plate, and shell length in mm. Without blanks the site cannot blank-correct; without lengths it cannot size-normalize.
readings.csv
One row per well per time point (long format). Comma- or tab-separated, with a header row. Column order does not matter.
Example (long format)
Wide format is also accepted by the uploader
One row per well, with one column per time point named by the hour (0, 1, 2 or T0, T1 or h0, h1). The uploader converts it to long format; the submission package is always long.
experiment.json
Example
What the site calculates
| Value | Definition |
|---|---|
| Fold change | fluorescence at hour t ÷ fluorescence of the same well at hour 0 |
| Blank-corrected fold change | fold change − mean fold change of the blank wells on the same plate at the same hour |
| Per mm | blank-corrected fold change ÷ shell length in mm (the paper's "metabolism") |
| Rate | blank-corrected fold change at the last reading ÷ hours elapsed |
Rules the validator enforces
sample_idis unique within the experiment, and each well has one reading per hour.typeissampleorblank. Empty shells and other controls are samples with agrouplabel.platenames the set of wells that share blanks. If blanks were run per temperature or per day, give each set its own plate name.- Every well has a positive reading at hour 0 and at least two readings. Empty fluorescence cells are skipped.
temperature_cis present for every sample. For two-phase designs, record the stress temperature and describe the schedule intemperature_profile.- Wells you want kept but hidden by default (spilled, saturated, empty shell) get a reason in
excluded.
About
This site is a static page served from the docs/ folder of its GitHub repository. It has no server and no database: the published data are bundled as one file, and everything else happens in your browser.
Source of the published data
Huffmyer AS, Ozguner N, Baird M, Elvrum C, Kounellas C, Dicksion D, White SJ, Plough L, Gavery MR, Krebs N, Walton W, Small J, Pitsenbarger M, Ealy-Whitfield H, Roberts S. 2026. From blue to pink: resazurin as a high-throughput proxy for metabolic rate in oysters. PeerJ 14:e21542. doi.org/10.7717/peerj.21542
Raw plate files came from RobertsLab/resazurin-assay-development and RobertsLab/vims-resazurin. The conversion scripts are in scripts/import_peerj21542/.
Adding an experiment permanently
- Use to check the files and download the submission package.
- Fork the repository and put the two files in
data/experiments/<id>/. - Open a pull request. A GitHub Action runs
scripts/validate.py; after merge it rebuildsdocs/data/db.jsand the site updates.
Caveats
Fold change depends on plate reader gain, resazurin volume per animal, and the temperature of the solution at the hour-0 read, so absolute values differ between studies for reasons other than biology. Compare shapes and within-study contrasts first, and treat cross-study differences in level with care.