How do you design a 96-well plate layout?
Count the wells first: compounds x concentrations x replicates, plus the control and blank wells each plate needs. Then decide how many wells are usable. The planner fills each plate with its controls first, then each compound's replicate series with concentrations running along the row.
Worked example: 4 compounds x 8 concentrations x 3 replicates = 96 sample wells. On a 96-well plate with the edge wells left empty, 60 wells are usable; with 4 negative and 4 positive control wells per plate, 52 remain for samples, so the experiment needs 2 plates.
Why leave edge wells empty?
Wells on the outside of a plate can behave differently from inner wells, for example through evaporation, so many labs fill them with buffer or leave them out of the analysis. Excluding them costs capacity: 36 of 96 wells, or 76 of 384. The planner shows the effect on the plate count.
Where should controls go on a plate?
On every plate, so each plate can be normalized and its quality checked, for example with the Z′-factor described by Zhang and colleagues (1999). This planner places them first in a fixed block. Many labs randomize or interleave positions to limit position effects; treat the layout as a starting point and adjust it to your assay.
Frequently asked questions
How many wells are in a 384-well plate and how are they labeled?
384 wells in 16 rows (A to P) and 24 columns (1 to 24), so the first well is A1 and the last is P24. A 96-well plate has 8 rows (A to H) and 12 columns.
How many usable wells are there without edges?
60 of 96 on a 96-well plate and 308 of 384 on a 384-well plate.
Can I export the plate map?
Yes. Download the layout as CSV with plate, well, content, compound, concentration index and replicate, which opens in Excel and other spreadsheet tools.
Should replicates be adjacent or spread out?
Adjacent replicates are easier to pipette; spread or randomized replicates reduce position effects. Choose based on your assay's known plate effects.
How do I prepare the concentrations?
Use the Serial Dilution Calculator to plan the series, then place it with this planner.
Is anything I enter saved or sent?
No. The calculator runs in your browser. Nothing you type is saved, sent to BioBridgeX or added to the page address, and analytics never see your numbers.
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Sources
- Zhang JH, Chung TD, Oldenburg KR. A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen 1999;4(2):67-73
- Markossian S et al., eds. Assay Guidance Manual. Eli Lilly & Company and NCATS, 2004-
Check every result before use. Formulas assume ideal conditions; follow your validated lab procedures and the reagent supplier's instructions. Facts on this page last checked 27 October 2026.
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