Why our first product starts with oxygen.

The question every spheroid raises

A spheroid is a small ball of cells grown in the lab. It is a useful model because cells in a ball behave more like cells in tissue than cells spread flat on a dish. It also raises a question that a flat dish never does: can oxygen reach the middle?

Oxygen enters from the surface. Cells near the surface use it first, so cells deeper in must live on what is left. Estimating how fast the cells in a spheroid consume oxygen is a standard step in explaining why the centre can run short^1,3. If too little reaches the centre, those cells become short of oxygen, and some may die. The outcome depends on the size of the spheroid, the cell type, the oxygen level in the incubator, and how long the culture runs.

Why the wait is the problem

Today the usual way to find out is to grow the spheroid and look. Every change to size, cell type or oxygen level normally means another culture of 7 to 14 days to see whether the centre survives. That is a typical range rather than a rule, and the real time depends on the cell type and the protocol.

Consider a lab that wants to compare three sizes at two oxygen levels. That is six cultures, each taking 7 to 14 days, before anyone has changed the cell type or the culture time.

The slow part of the work is not the thinking. It is waiting to find out whether the thinking was right.

Why simulation has stayed out of reach

Powerful simulation tools exist, but they fall into two groups. Some are priced for large pharma. Others are open source and capable, but they need programming, installation and specialist knowledge that most tissue engineering labs do not have on staff.

That leaves many academic labs and small biotechs with a capable idea and no practical way to use it. We think that is a software problem, and a solvable one.

What Spherix answers first

Spherix is browser based simulation software for 3D tissue engineering. Its first module predicts how oxygen reaches the cells inside a spheroid, and where cells become starved of oxygen or die. The full simulation is built on PhysiCell, an open source, peer reviewed simulator that follows every cell as its own agent².

The predictions

• Viable rim: the thickness of the living outer layer
• Hypoxic shell: the region short of oxygen
• Necrotic core: the dead centre, if one forms, and when it first appears
• Oxygen level at the centre and across the spheroid
• Viable volume, and the largest diameter that stays fully viable under the chosen conditions

Every result comes with a 90% uncertainty range, and every prediction corresponds to a lab assay that labs already run, such as live/dead imaging, histology, hypoxia staining or oxygen probes. That means a prediction can be checked.

Spherix is a decision support tool for ranking and narrowing designs before wet lab work. It is not a replacement for experiments, and it is for research use only.