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Zebrafish Experiment Yield Planner.

Calculate how many eggs to collect and breeding pairs to set up for your zebrafish experiment endpoint. Models stage-by-stage attrition from fertilization to target dpf.

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Validated2026-04-06
CitableMethods and citation included

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Load example Experiment Yield data to see the full workflow

Configuration

1 dpf90 dpf
30%100%
0%5000%

When to use

  • Planning egg collections for a specific experimental endpoint (e.g., 96 larvae at 5 dpf)
  • Calculating how many breeding pairs to set up for a single experiment
  • Understanding stage-by-stage attrition to identify where losses will occur
  • Estimating overshoot needed for transgenic or mutant lines with higher attrition

Do not use for

  • For ongoing colony management and weekly production — use the Breeding Colony Size Planner instead
  • For determining housing density after larvae are collected — use the Stocking Density Calculator
  • For genetic cross ratios or genotyping yield — this models viability, not Mendelian genetics

Calibrate fertilization rate to your colony

The default 70% fertilization rate reflects typical wild-type colonies. If you routinely achieve 80–90%, adjust upward. If your transgenic line runs at 40–50%, adjust down. Small differences in fertilization rate compound significantly when back-calculating to eggs needed.

Plate format determines your target N

Choose your target N based on full plate utilization: 24, 48, 96, or 384. Partial plates waste resources and complicate statistical analysis. If you need replicates across multiple plates, multiply accordingly (e.g., 3 plates of 96 = target N of 288).

Later endpoints need substantially more eggs

Each developmental stage adds cumulative losses. A 5 dpf endpoint needs ~70% more eggs than target N, while a 14 dpf endpoint needs ~90% more. A 90 dpf (adult) endpoint can require 2–3× the target in starting eggs. Plan accordingly and stagger collections if needed.

Safety margin is not optional for critical experiments

Even with perfect historical attrition data, individual spawns vary. A 20% safety margin is minimum for routine experiments. Use 30–50% for critical experiments, new strains, or when you cannot repeat the collection if numbers fall short.

1

Method

Survival at any dpf is interpolated linearly between published checkpoint rates (1, 3, 5, 7, 14, 30, 90 dpf). Eggs needed = ceil(targetN ×\times (1 + safetyMargin) / (fertilizationRate ×\times survivalAtEndpoint)). Starting pairs = ceil(eggsNeeded / (clutchSize ×\times spawningSuccessRate)). Default survival rates are from literature consensus for wild-type zebrafish under standard husbandry.

2

Validated

Last validated 2026-04-06. Calculations are designed for planning and documentation support; verify procurement decisions against manufacturer specifications or institutional SOPs.

3

How to cite

How to Cite

ConductScience Zebrafish Experiment Yield Planner (v1.0). ConductScience, Inc. 2026. Available at: https://conductscience.com/tools/zebrafish-experiment-yield-planner

Kimmel CB et al. Stages of embryonic development of the zebrafish. Dev Dyn. 1995;203(3):253-310.

Westerfield M. The Zebrafish Book, 5th Ed. University of Oregon Press. 2007.

Zebrafish Survival Curves in the Laboratory

Zebrafish attrition follows a predictable pattern under standard laboratory conditions. The steepest losses occur during early development:

Critical loss points: - 0–1 dpf: ~5% loss from unfertilized eggs missed during sorting and early developmental arrest - 1–3 dpf: ~5% loss from gastrulation/segmentation failures and morphological abnormalities - 3–5 dpf: ~5% loss around swim bladder inflation — larvae that fail to inflate cannot feed effectively - 5–7 dpf: ~5% loss at the "point of no return" where yolk reserves are exhausted and larvae must actively feed - 7–14 dpf: ~5% loss during the transition to external feeding and early juvenile growth

These rates assume wild-type fish under optimal conditions. Mutant lines, suboptimal water quality, or crowding can double or triple these losses at each stage. Always calibrate with your own colony data when available.

Experimental Design for Larvae Assays

Most zebrafish larvae experiments use multiwell plate formats:

  • 24-well plates: 1 larva per well, behavioral tracking with larger arena, preferred for complex locomotor assays
  • 48-well plates: Higher throughput, adequate for basic activity monitoring
  • 96-well plates: Standard format for drug screens and high-throughput phenotyping at 5 dpf
  • 384-well plates: Emerging format for ultra-high-throughput chemical screens
Key planning considerations: - Plate format determines your target N (must fill complete plates for balanced experimental design) - Include untreated and vehicle controls — typically 1 control column per treatment plate - Larvae should be size-matched and morphologically normal at plating - Plan to collect 2–3× more larvae than plate capacity to allow selection of healthy, staged animals - Stagger egg collections across consecutive days to ensure adequate numbers despite daily variability

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