Understand the relationship
The reasoning behind the result
Yield and recovery require printed denominators
Yield = R/A; instrument-count recovery = R/S
Cell-separation literature uses recovery both for recovered target cells over starting target cells and for recovered target cells over the instrument's reported sort count. Other sources call the first relationship yield and reserve recovery for the second.
The workbench therefore prints both formulas and avoids an unlabeled recovery percentage. A, S and R remain three distinct checkpoints even when two happen to contain the same number.
Starting target cells can be entered or reconstructed
A = Cstart × Vstart × ftarget,start
A direct starting-target total can come from an external absolute count. The measured-suspension path instead multiplies entered total-cell concentration by entered volume and the entered starting target fraction.
The calculator does not decide the target gate, infer concentration from event percentages or correct the starting record for unmeasured losses.
An electronic sort count is not a recovered count
Reported sort fraction = S/A
Sorter software can report target particles accepted or deposited according to the instrument's electronic sort logic. That record is useful for accounting, but it does not confirm physical arrival in the collection vessel.
Recovery against S therefore needs an independent physical target count R from the collected material. The workbench does not model drop delay, coincidence, abort logic, stream placement or collection loss.
Target fraction and viability answer different questions
Post-sort target fraction = R/T; viable-target yield = V/A
Recovered target cells R divided by all recovered cells T describes the entered post-sort target fraction, often reported as purity. Viable target cells V divided by R describes viability within that target count.
Viable-target yield V/A combines the entered viability record with the starting-target denominator. It does not establish function, sterility, clonogenicity or fitness for a downstream application.
Multiple fractions are pooled through counts
Rtotal = Σ(Tj × fj); Vtotal = Σ(Tj × fj × vj)
Each collection fraction contributes its recovered total Tj, target fraction fj and target viability vj. Summing target and viable-target counts before forming percentages gives the correct count-weighted aggregate.
Directly averaging percentages would give small and large collection fractions equal influence and can misstate the pooled result.
Follow the numbers
Reconcile a measured starting suspension and collected suspension
- Start with 2,000,000 total cells/mL across 5 mL: 10,000,000 entered starting cells.
- Apply the entered 12% target fraction to reconstruct 1,200,000 starting target cells.
- The sorter reports 900,000 deposited target cells, or 75% of the reconstructed starting target count.
- The collection contains 480,000 total cells/mL across 1.5 mL: 720,000 recovered total cells. At an entered 95% target fraction, 684,000 are recovered target cells.
- Recovered-target yield is 684,000/1,200,000 = 57%; instrument-count recovery is 684,000/900,000 = 76%. An entered 90% target viability gives 615,600 viable target cells and a 51.3% viable-target yield.
The 57% starting-target yield, 76% instrument-count recovery, 95% post-sort target fraction, 90% target viability and 7.2% total-cell recovery remain separate results.
Quick guide
How to use this calculator
- Declare the target population and the count, viability, gate, sample and sort scope shared by the checkpoints.
- Enter starting target cells directly or reconstruct them from a starting total-cell concentration, suspension volume and target fraction.
- Copy the sorter-reported deposited target count without substituting it for a physical post-sort count. Enter the collection as direct totals, a measured suspension or multiple fractions.
- Read each named percentage with its printed denominator and inspect the checkpoint and collection ledgers before comparing runs.
Calculation method
Calculation and interpretation
Audit one cell-sorting mass balance without treating an electronic sort counter, post-sort count, viability measurement or target fraction as the same quantity.
Recovered-target yield = 100R/A; instrument-count recovery = 100R/S; instrument-reported sort fraction = 100S/A; viable-target yield = 100V/A. Here A is starting target cells, S is the sorter-reported deposited target count, R is physically recovered target cells and V is viable recovered target cells.
Worked example
Reconcile a measured starting suspension and collected suspension
The 57% starting-target yield, 76% instrument-count recovery, 95% post-sort target fraction, 90% target viability and 7.2% total-cell recovery remain separate results.
Recovered-target yield = 100R/A; instrument-count recovery = 100R/S; instrument-reported sort fraction = 100S/A; viable-target yield = 100V/A. Here A is starting target cells, S is the sorter-reported deposited target count, R is physically recovered target cells and V is viable recovered target cells.
Supported inputs
Precision and limits
Entered summaries only
The workbench does not read FCS files, gate cells, identify targets, count a suspension, determine viability, verify sorter counters or inspect collection vessels.
Matched scopes remain external
Starting, instrument and recovered records must refer to a defensibly matched target definition and sample scope. Subsampling, dilution, residual volume, transfers, reruns and excluded material must already be reconciled by the visitor's method.
Values above 100% are retained
A ratio above 100% may reflect counting uncertainty, subsampling, unmatched gates or scopes, concentration/volume error or another record problem. It is displayed for audit and is neither capped nor declared physically validated.
No sorter-performance model
The outputs do not calculate Rmax, predict Lindmo efficiency, diagnose drop delay, recommend a sort mode, nozzle, pressure, event rate, collection vessel or instrument setting, or assign a cause to an accounting difference.
No downstream suitability conclusion
Post-sort target fraction and viability do not establish function, clonogenicity, sterility, assay success, clinical suitability, treatment response or statistical significance.
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