Sooner or later a fab asks you for GDSII, and if you came to microfluidics from biology or chemistry rather than from semiconductors, the request arrives without a manual. This is the manual — no layout-editor jargon, and an explicit list of the mistakes that cost a mask run.
What GDSII is, and why microfluidics uses it
GDSII is a binary format from integrated-circuit layout. It was never designed for fluidics; microfluidics inherited it because microfluidics is made in the same cleanrooms, on the same mask writers, by the same vendors. If your chip starts as a photomask — and most do — the mask shop's software speaks GDSII.
A GDSII file contains one thing: flat two-dimensional polygons, organised into cells and layers. That is the whole model. Everything else you might want to say about your chip has to be carried somewhere else.
There is no depth in the file
This matters because depth is the dimension your hydraulic resistance is most sensitive to. You can hand a fab a perfect GDSII and still receive a chip whose flow is wrong, because the depth you assumed and the depth they ran were different numbers that were never written down in the same place.
So state the depth in the purchase order, in the drawing notes, and in the filename if you have to. And if your chip has two different depths, that is two mask levels and a multi-step process — say so explicitly, because the file will not.
They are mask levels, not decoration
Each polygon sits on a numbered layer, optionally with a datatype. In a CAD tool layers feel like a convenience for organising your drawing. In a fab they are instructions. Nobody can guess your numbering — send a layer table with the file. Three lines of text that prevent a week of email.
| Layer | Datatype | Meaning | Process step |
|---|---|---|---|
| 1 | 0 | Fluidic channels, 50 µm deep | SU-8 mould, single exposure |
| 2 | 0 | Inlet / outlet ports, Ø 1.0 mm | Punched after bonding |
| 10 | 0 | Alignment marks | All levels |
| 63 | 0 | Die outline — not etched | Reference only |
The error that silently scales your chip by 1000
GDSII stores coordinates as integers, with two header numbers telling you what an integer means: the user unit (typically 1 µm) and the database unit (typically 1 nm). The grid is the database unit, so with the usual settings your geometry snaps to 1 nm — fine for anything fluidic.
The failure mode is importing a file written on a different assumption, so a 10 mm die arrives as a 10 µm speck or a 10 m monster. Always check one known dimension after import — the die outline is ideal — before you look at anything else. Five seconds, and it catches the only unit error that matters.
Curves do not exist
GDSII has polygons. No arcs, no splines, no circles. Every curve you drew is approximated by straight segments when the file is written, and the number of segments is a setting somebody chose.
Too coarse and a smooth serpentine becomes a faceted one — cosmetically ugly, and in tight bends it can change the local cross-section enough to matter. Too fine and the file becomes enormous and the mask writer slows down. There is no point resolving a curve to 10 nm when the process holds ±2 µm: pick a chord tolerance related to what the process can actually do.
Also check that round ports are still round enough after export. A 1 mm inlet rendered as a twelve-sided polygon is a port that will not seal predictably against a standard fitting.
What the fab needs that the file cannot carry
- Polarity. Are the polygons the channels, or the material around them? Both conventions exist. Say which.
- Material and process. PDMS from an SU-8 mould, COC injection moulding and glass wet etch do not share a minimum feature, a sidewall or a corner radius.
- The tolerance you actually care about. Not "±1 µm everywhere" — tell them which dimension is critical. A fab can usually hold one dimension tightly if it knows which one.
- Bonding and sealing. Bond width, surface finish, anything that must stay clear.
- Quantity and intent. Five prototypes and five thousand parts are different conversations about the same drawing.
Is GDSII even right for you?
| Format | Use it when | Watch out for |
|---|---|---|
| GDSII | Photomask writing; anything cleanroom-adjacent | 2D only, no depth, no curves |
| DXF | Many soft-lithography and laser services prefer it | Version chaos; units often ambiguous |
| STEP | CNC, moulding, anything genuinely 3D or assembled | Large files; overkill for a single mask level |
| STL | 3D printing, visualisation | Tessellated surfaces — not a precise solid |
Ask the fab first. Sending the format they already use removes an entire category of problem.
Seven checks
- Re-import your own export and measure one known dimension.
- Confirm the die outline is where you think it is, and that nothing extends past it.
- Check the layer table matches the file, layer by layer.
- Look at the tightest curve and the smallest port at high zoom. Faceted?
- Find your smallest feature and your smallest gap; compare both against the process minimum.
- Write the depth down, in the covering email, explicitly.
- Say which dimension is critical, and why.
Draw it, check it, export it
Open a sample chip in your browser, run the manufacturing checks against a process profile, and look at what goes into the export package — before you ever talk to a fab.
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