Cryopreservation & IVF Calculator

What you’re building

Cryopreservation is insurance for your mouse colony. Instead of keeping a rare or expensive line alive as a breeding colony indefinitely — burning through per diem costs and cage space — you freeze sperm and recover the line later by IVF when you need it. The GEAM facility does this as a service, archiving dozens of lines per year.

The problem: every freeze session involves mental math. How much cryoprotectant do you dilute? What post-thaw motility should you expect for this strain? How many females do you superovulate to get enough oocytes for a recovery? Right now, the answers live in someone’s head, a dog-eared protocol binder, or scattered across old lab notebooks.

You are going to build a calculator that centralizes all of that in one browser tab.

By the end of this lesson you will have a standalone cryopreservation and IVF calculator that runs entirely in the browser. It loads embedded historical freeze/thaw data, calculates media dilution volumes, estimates post-thaw viability based on past performance, and plans IVF recovery sessions. You will build it by giving a single prompt to an LLM CLI tool.

Who this is for

• GEAM cryopreservation technicians who perform freeze and thaw sessions weekly and need quick dilution calculations and viability benchmarks.
• Colony managers planning line archival or recovery who need to estimate how many females to superovulate and how many straws to thaw.
• PIs and lab managers who want historical viability data at a glance to decide whether to collect fresh sperm and try a different cryoprotectant protocol for lines with poor past performance.

The showcase

Here is what the finished calculator looks like once you open the HTML file in a browser:

• Historical viability dashboard showing a bar chart of post-thaw motility rates across all archived strains. Each bar is color-coded: green (>50% motility), amber (20-50%), red (<20%).
• Dilution calculator with input fields for stock cryoprotectant concentration, desired working concentration, and final volume. Outputs the exact volumes of stock solution and diluent needed.
• Post-thaw viability estimator where you select a strain and see its historical average motility with confidence range, plus a go/no-go recommendation.
• IVF planning section with inputs for number of straws to thaw, expected motility, number of females to superovulate, expected oocyte yield per female, and fertilization rate. Outputs the expected number of 2-cell embryos and a recommendation on whether to proceed.
• Summary card with a go/no-go recommendation based on all inputs, with clear reasoning.

Everything runs client-side. No data leaves the browser.

The prompt

Open your terminal Terminal The app where you type commands. Mac: Cmd+Space, type "Terminal". Windows: open WSL (Ubuntu) from the Start menu. Full lesson → , navigate to a project folder project folder A directory on your computer where the tool lives. Create one with "mkdir my-project && cd my-project". Full lesson → , start your AI CLI tool AI CLI tool Claude Code, Gemini CLI, or Codex CLI — a command-line AI that reads files, writes code, and runs commands. Full lesson → (e.g., by typing claude), and paste this prompt:

Build a single self-contained HTML file called cryo-calculator.html that serves as
a cryopreservation and IVF calculator for a mouse facility. Requirements:

1. EMBEDDED HISTORICAL DATA
   Preload the following freeze/thaw history as a JavaScript array:
   [
     { strain: "B6-Cre", dateFrozen: "2025-06-15", strawsFrozen: 12, preMotility: 85, postMotility: 62, cryoprotectant: "DMSO", coolingRate: "slow-freeze" },
     { strain: "B6-Cre", dateFrozen: "2025-09-20", strawsFrozen: 10, preMotility: 80, postMotility: 58, cryoprotectant: "DMSO", coolingRate: "slow-freeze" },
     { strain: "129-KO", dateFrozen: "2025-07-10", strawsFrozen: 8, preMotility: 78, postMotility: 45, cryoprotectant: "DMSO", coolingRate: "slow-freeze" },
     { strain: "129-KO", dateFrozen: "2025-11-05", strawsFrozen: 10, preMotility: 82, postMotility: 42, cryoprotectant: "glycerol", coolingRate: "slow-freeze" },
     { strain: "BALB-Flox", dateFrozen: "2025-08-22", strawsFrozen: 15, preMotility: 90, postMotility: 71, cryoprotectant: "DMSO", coolingRate: "slow-freeze" },
     { strain: "BALB-Flox", dateFrozen: "2026-01-10", strawsFrozen: 12, preMotility: 88, postMotility: 68, cryoprotectant: "DMSO", coolingRate: "slow-freeze" },
     { strain: "NSG-tdTom", dateFrozen: "2025-10-01", strawsFrozen: 6, preMotility: 75, postMotility: 18, cryoprotectant: "glycerol", coolingRate: "slow-freeze" },
     { strain: "NSG-tdTom", dateFrozen: "2026-02-14", strawsFrozen: 8, preMotility: 72, postMotility: 15, cryoprotectant: "glycerol", coolingRate: "slow-freeze" },
     { strain: "FVB-GFP", dateFrozen: "2025-05-30", strawsFrozen: 10, preMotility: 88, postMotility: 55, cryoprotectant: "DMSO", coolingRate: "slow-freeze" },
     { strain: "CD1-WT", dateFrozen: "2025-12-08", strawsFrozen: 20, preMotility: 92, postMotility: 74, cryoprotectant: "DMSO", coolingRate: "slow-freeze" },
     { strain: "CD1-WT", dateFrozen: "2026-01-25", strawsFrozen: 18, preMotility: 90, postMotility: 70, cryoprotectant: "DMSO", coolingRate: "slow-freeze" },
     { strain: "Swiss-KI", dateFrozen: "2025-09-12", strawsFrozen: 8, preMotility: 70, postMotility: 12, cryoprotectant: "glycerol", coolingRate: "slow-freeze" }
   ]

2. HISTORICAL VIABILITY DASHBOARD
   - Grouped bar chart (Chart.js) showing pre-freeze vs post-thaw motility for
     each freeze record, sorted by strain name
   - Color-code post-thaw bars: green if >50%, amber if 20-50%, red if <20%
   - Show strain average motility as a horizontal reference line per strain group
   - Display average post-thaw motility per strain in summary cards above the chart

3. DILUTION CALCULATOR
   - Input fields: stock concentration (%), desired working concentration (%),
     final volume needed (mL)
   - Calculate and display: volume of stock solution (mL), volume of diluent (mL)
   - Formula: V_stock = (C_working x V_final) / C_stock; V_diluent = V_final - V_stock
   - Common presets: "10% DMSO from 100% stock", "15% glycerol from 100% stock",
     "5% DMSO from 50% stock" — clicking a preset fills in the fields
   - Show a warning if calculated stock volume exceeds final volume (impossible dilution)

4. POST-THAW VIABILITY ESTIMATOR
   - Dropdown to select a strain from the historical data
   - Show that strain's historical average post-thaw motility with min/max range
   - Show number of previous freeze records for confidence context
   - Go/no-go recommendation: green "Good candidate" if avg >50%, amber "Proceed
     with caution" if 20-50%, red "Poor viability — collect fresh sperm and
     freeze with different protocol" if <20%
   - If strain has only 1 record, show a "Low confidence — only 1 data point" note

5. IVF PLANNING SECTION
   - Inputs: number of straws to thaw, expected post-thaw motility (auto-fill from
     strain selection), number of females to superovulate, expected oocytes per
     female (default 25), expected fertilization rate (default 60%)
   - Calculate: total expected motile sperm, total expected oocytes, expected
     2-cell embryos (oocytes x fertilization rate), expected live pups (2-cell
     embryos x 30% implantation rate)
   - Summary card: "Thaw X straws → Y motile doses → Z oocytes from N females →
     W expected 2-cell embryos → V expected pups"
   - Go/no-go: green if expected pups >= 10, amber if 5-9, red if <5

6. DESIGN
   - Dark theme: background #0f172a, cards #1e293b, text #e2e8f0, accent #10b981
   - Clean sans-serif font (Inter from Google Fonts CDN)
   - Responsive layout, calculator sections in a clear top-to-bottom flow
   - Go/no-go badges with distinct colors and icons
   - Input fields with clear labels and units

7. TECHNICAL
   - Pure HTML/CSS/JS in one file, no build step
   - Chart.js loaded from CDN (https://cdn.jsdelivr.net/npm/chart.js)
   - All calculations in real-time as inputs change (no submit button needed)
   - Input validation: no negative numbers, concentrations 0-100%, volumes > 0

What you get

After the LLM finishes (typically 60-90 seconds), you will have a single file: cryo-calculator.html. Open it in any browser.

Expected output structure

cryo-calculator.html    (~500-700 lines)

You should see:

1. Strain summary cards at the top showing average post-thaw motility for each strain. CD1-WT should show ~72%, B6-Cre ~60%, NSG-tdTom ~16.5%, Swiss-KI ~12%.
2. A grouped bar chart with paired bars (pre-freeze in blue, post-thaw in colored by threshold) for all 12 freeze records. NSG-tdTom and Swiss-KI bars should be red. BALB-Flox and CD1-WT bars should be green.
3. The dilution calculator with three input fields. Click the “10% DMSO from 100% stock” preset and it should show: stock volume = 1 mL, diluent = 9 mL (for a 10 mL final volume).
4. The viability estimator — select “NSG-tdTom” from the dropdown and you should see an average of ~16.5% motility with a red “Poor viability” recommendation. Select “BALB-Flox” and you should see ~69.5% with a green “Good candidate” badge.
5. The IVF planning section — with default values, it should calculate the full pipeline from straws to expected pups and show a go/no-go recommendation.

If something is off

How it works (the 2-minute explanation)

You do not need to understand every line of the generated code, but here is the mental model:

1. The dilution formula is C1 x V1 = C2 x V2, rearranged to find V1 (volume of stock to add). The diluent volume is simply the final volume minus the stock volume. This is the same formula from general chemistry.
2. Historical viability is just descriptive statistics: compute the mean, min, and max of post-thaw motility for each strain. The color thresholds (50%, 20%) turn these numbers into actionable recommendations.
3. IVF planning chains a series of multiplications: straws x motile fraction = motile sperm doses, females x oocytes/female = total oocytes, oocytes x fertilization rate = 2-cell embryos, embryos x implantation rate = expected pups. Each step has uncertainty, but the chain gives a useful planning estimate.
4. Chart.js conditional coloring assigns a different backgroundColor to each bar based on its value, using a simple map() over the data array with threshold checks.

Customize it

The base calculator is useful as-is, but here are single-prompt extensions that make it more powerful:

Add strain-specific protocol recommendations

Add a "Protocol Advisor" section. Based on the historical data, recommend the best
cryoprotectant and cooling rate for each strain. Compare average post-thaw motility
across protocols used for the same strain. If a strain has been frozen with both
DMSO and glycerol, show which performed better as a clear recommendation card with
the percent difference. If only one protocol has been tried, suggest trying the
alternative and show what other similar strains achieved with it.

Add cost estimator

Add a "Cost Estimator" panel to the IVF planning section. Include these cost
inputs with default values: superovulation hormones per female ($15), IVF media
and supplies per session ($50), transfer surgery per recipient ($75), per diem
cage cost per day ($1.50), expected days to genotype (21). Calculate the total cost
of a recovery attempt and compare it to the cost of maintaining a live breeding
colony for 6 months. Show a break-even analysis: "Recovery costs $X. Maintaining
a live colony costs $Y per month. Cryopreservation pays for itself after Z months."

Add batch comparison view

Add a "Batch Comparison" tab that lets me select two freeze sessions for the same
strain and compare them side by side. Show pre-freeze motility, post-thaw motility,
cryoprotectant used, date frozen, and any differences highlighted. Include a small
line chart showing that strain's motility trend over time (X-axis: freeze dates,
Y-axis: post-thaw motility) to spot whether the protocol is improving or degrading.

Try it yourself

1. Open your CLI tool in an empty folder.
2. Paste the main prompt from above.
3. Open the generated cryo-calculator.html in your browser.
4. Try the dilution calculator with different concentrations.
5. Select “NSG-tdTom” in the viability estimator and note the red warning — then select “CD1-WT” and see the green recommendation.
6. Pick one customization from the list above and add it.

If your facility freezes even a few mouse lines per year, this tool standardizes the decision-making process. Save it, share it with the cryo team.

Key takeaways

• One prompt, one tool: a detailed prompt with embedded historical data produces a working cryopreservation calculator in under 2 minutes.
• Single-file HTML tools run anywhere — on the facility office computer, on a laptop in the vivarium, on a PI’s desktop during a meeting. No installation, no dependencies.
• Historical viability data transforms anecdotal experience into evidence-based decisions — tracking post-thaw motility across strains and protocols reveals patterns that individual technicians might not notice.
• The dilution formula is universal — the same C1V1 = C2V2 pattern applies to buffer preparation, drug dosing, media formulation, and any concentration-based calculation.
• Go/no-go recommendations reduce cognitive load — instead of interpreting numbers, the tool gives a clear green/amber/red signal. The user can still see the underlying data, but the recommendation surfaces the actionable conclusion immediately.

What’s next

In the next lesson, you will build a Stable Isotope Batch QC Dashboard — a tool that flags instrument drift, applies reference corrections to delta values, and visualizes measurement variance across analytical runs. Same pattern: one prompt, one HTML file, immediate utility for the stable isotope facility.