diff --git a/Cargo.lock b/Cargo.lock
index 95e00df9..77e85b6b 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -197,9 +197,9 @@ checksum = "37b2a672a2cb129a2e41c10b1224bb368f9f37a2b16b612598138befd7b37eb5"
 
 [[package]]
 name = "cc"
-version = "1.2.1"
+version = "1.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fd9de9f2205d5ef3fd67e685b0df337994ddd4495e2a28d185500d0e1edfea47"
+checksum = "f34d93e62b03caf570cccc334cbc6c2fceca82f39211051345108adcba3eebdc"
 dependencies = [
  "jobserver",
  "libc",
@@ -648,12 +648,12 @@ dependencies = [
 
 [[package]]
 name = "errno"
-version = "0.3.9"
+version = "0.3.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "534c5cf6194dfab3db3242765c03bbe257cf92f22b38f6bc0c58d59108a820ba"
+checksum = "33d852cb9b869c2a9b3df2f71a3074817f01e1844f839a144f5fcef059a4eb5d"
 dependencies = [
  "libc",
- "windows-sys 0.52.0",
+ "windows-sys 0.59.0",
 ]
 
 [[package]]
@@ -858,7 +858,7 @@ dependencies = [
 [[package]]
 name = "hugr"
 version = "0.13.3"
-source = "git+https://github.com/CQCL/hugr.git#bcac68d3c147e960b921927f58b2fca8c86ccdc7"
+source = "git+https://github.com/CQCL/hugr.git#163b211cfb8b87a7b0a6a12c8141217e0c052dd5"
 dependencies = [
  "hugr-core",
  "hugr-passes",
@@ -867,7 +867,7 @@ dependencies = [
 [[package]]
 name = "hugr-cli"
 version = "0.13.3"
-source = "git+https://github.com/CQCL/hugr.git#bcac68d3c147e960b921927f58b2fca8c86ccdc7"
+source = "git+https://github.com/CQCL/hugr.git#163b211cfb8b87a7b0a6a12c8141217e0c052dd5"
 dependencies = [
  "clap",
  "clap-verbosity-flag",
@@ -882,7 +882,7 @@ dependencies = [
 [[package]]
 name = "hugr-core"
 version = "0.13.3"
-source = "git+https://github.com/CQCL/hugr.git#bcac68d3c147e960b921927f58b2fca8c86ccdc7"
+source = "git+https://github.com/CQCL/hugr.git#163b211cfb8b87a7b0a6a12c8141217e0c052dd5"
 dependencies = [
  "bitvec",
  "bumpalo",
@@ -914,7 +914,7 @@ dependencies = [
 [[package]]
 name = "hugr-passes"
 version = "0.13.3"
-source = "git+https://github.com/CQCL/hugr.git#bcac68d3c147e960b921927f58b2fca8c86ccdc7"
+source = "git+https://github.com/CQCL/hugr.git#163b211cfb8b87a7b0a6a12c8141217e0c052dd5"
 dependencies = [
  "hugr-core",
  "itertools 0.13.0",
@@ -1203,9 +1203,9 @@ checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe"
 
 [[package]]
 name = "libc"
-version = "0.2.166"
+version = "0.2.167"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c2ccc108bbc0b1331bd061864e7cd823c0cab660bbe6970e66e2c0614decde36"
+checksum = "09d6582e104315a817dff97f75133544b2e094ee22447d2acf4a74e189ba06fc"
 
 [[package]]
 name = "linux-raw-sys"
@@ -1581,9 +1581,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3"
-version = "0.22.6"
+version = "0.23.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f402062616ab18202ae8319da13fa4279883a2b8a9d9f83f20dbade813ce1884"
+checksum = "f54b3d09cbdd1f8c20650b28e7b09e338881482f4aa908a5f61a00c98fba2690"
 dependencies = [
  "cfg-if",
  "indoc",
@@ -1599,9 +1599,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-build-config"
-version = "0.22.6"
+version = "0.23.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b14b5775b5ff446dd1056212d778012cbe8a0fbffd368029fd9e25b514479c38"
+checksum = "3015cf985888fe66cfb63ce0e321c603706cd541b7aec7ddd35c281390af45d8"
 dependencies = [
  "once_cell",
  "target-lexicon",
@@ -1609,9 +1609,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-ffi"
-version = "0.22.6"
+version = "0.23.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9ab5bcf04a2cdcbb50c7d6105de943f543f9ed92af55818fd17b660390fc8636"
+checksum = "6fca7cd8fd809b5ac4eefb89c1f98f7a7651d3739dfb341ca6980090f554c270"
 dependencies = [
  "libc",
  "pyo3-build-config",
@@ -1619,9 +1619,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros"
-version = "0.22.6"
+version = "0.23.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0fd24d897903a9e6d80b968368a34e1525aeb719d568dba8b3d4bfa5dc67d453"
+checksum = "34e657fa5379a79151b6ff5328d9216a84f55dc93b17b08e7c3609a969b73aa0"
 dependencies = [
  "proc-macro2",
  "pyo3-macros-backend",
@@ -1631,9 +1631,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros-backend"
-version = "0.22.6"
+version = "0.23.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "36c011a03ba1e50152b4b394b479826cad97e7a21eb52df179cd91ac411cbfbe"
+checksum = "295548d5ffd95fd1981d2d3cf4458831b21d60af046b729b6fd143b0ba7aee2f"
 dependencies = [
  "heck",
  "proc-macro2",
@@ -1644,9 +1644,9 @@ dependencies = [
 
 [[package]]
 name = "pythonize"
-version = "0.22.0"
+version = "0.23.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "90fcf491425978bd889015d5430f6473d91bdfa2097262f1e731aadcf6c2113e"
+checksum = "91a6ee7a084f913f98d70cdc3ebec07e852b735ae3059a1500db2661265da9ff"
 dependencies = [
  "pyo3",
  "serde",
@@ -2133,10 +2133,11 @@ dependencies = [
 
 [[package]]
 name = "tket-json-rs"
-version = "0.6.2"
+version = "0.7.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "45811ae5d7deb7c7e14bbf031e75b2ab7db2154ed56d1ed2eb9bb28a0a0df4b8"
+checksum = "bbce51b8204122752da67c65d5cf13a9b8f09f10664d1fb40aa03f94bebdd1cb"
 dependencies = [
+ "derive_more 1.0.0",
  "pyo3",
  "pythonize",
  "serde",
@@ -2515,9 +2516,9 @@ dependencies = [
 
 [[package]]
 name = "webbrowser"
-version = "1.0.2"
+version = "1.0.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2e5f07fb9bc8de2ddfe6b24a71a75430673fd679e568c48b52716cef1cfae923"
+checksum = "ea9fe1ebb156110ff855242c1101df158b822487e4957b0556d9ffce9db0f535"
 dependencies = [
  "block2",
  "core-foundation",
diff --git a/Cargo.toml b/Cargo.toml
index 6a774821..e9f18c8a 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -37,9 +37,9 @@ hugr = "0.13.3"
 hugr-core = "0.13.3"
 hugr-cli = "0.13.3"
 portgraph = "0.12"
-pyo3 = "0.22.5"
+pyo3 = "0.23.2"
 itertools = "0.13.0"
-tket-json-rs = "0.6.2"
+tket-json-rs = "0.7.1"
 tracing = "0.1.37"
 portmatching = "0.3.1"
 bytemuck = "1.20.0"
diff --git a/tket2-py/src/circuit.rs b/tket2-py/src/circuit.rs
index a70e3559..3c939a20 100644
--- a/tket2-py/src/circuit.rs
+++ b/tket2-py/src/circuit.rs
@@ -30,7 +30,7 @@ pub use tket2::{Pauli, Tk2Op};
 
 /// The module definition
 pub fn module(py: Python<'_>) -> PyResult<Bound<'_, PyModule>> {
-    let m = PyModule::new_bound(py, "circuit")?;
+    let m = PyModule::new(py, "circuit")?;
     m.add_class::<Tk2Circuit>()?;
     m.add_class::<PyNode>()?;
     m.add_class::<PyWire>()?;
@@ -40,14 +40,14 @@ pub fn module(py: Python<'_>) -> PyResult<Bound<'_, PyModule>> {
     m.add_function(wrap_pyfunction!(render_circuit_dot, &m)?)?;
     m.add_function(wrap_pyfunction!(render_circuit_mermaid, &m)?)?;
 
-    m.add("HugrError", py.get_type_bound::<PyHugrError>())?;
-    m.add("BuildError", py.get_type_bound::<PyBuildError>())?;
-    m.add("ValidationError", py.get_type_bound::<PyValidationError>())?;
+    m.add("HugrError", py.get_type::<PyHugrError>())?;
+    m.add("BuildError", py.get_type::<PyBuildError>())?;
+    m.add("ValidationError", py.get_type::<PyValidationError>())?;
     m.add(
         "HUGRSerializationError",
-        py.get_type_bound::<PyHUGRSerializationError>(),
+        py.get_type::<PyHUGRSerializationError>(),
     )?;
-    m.add("TK1ConvertError", py.get_type_bound::<PyTK1ConvertError>())?;
+    m.add("TK1ConvertError", py.get_type::<PyTK1ConvertError>())?;
 
     Ok(m)
 }
diff --git a/tket2-py/src/circuit/convert.rs b/tket2-py/src/circuit/convert.rs
index 00d5404f..93fb1a8f 100644
--- a/tket2-py/src/circuit/convert.rs
+++ b/tket2-py/src/circuit/convert.rs
@@ -11,8 +11,8 @@ use itertools::Itertools;
 use pyo3::exceptions::{PyAttributeError, PyValueError};
 use pyo3::types::{PyAnyMethods, PyModule, PyString, PyTypeMethods};
 use pyo3::{
-    pyclass, pymethods, Bound, FromPyObject, PyAny, PyErr, PyObject, PyRefMut, PyResult,
-    PyTypeInfo, Python, ToPyObject,
+    pyclass, pymethods, Bound, FromPyObject, IntoPyObject, PyAny, PyErr, PyObject, PyRefMut,
+    PyResult, PyTypeInfo, Python,
 };
 
 use derive_more::From;
diff --git a/tket2-py/src/circuit/tk2circuit.rs b/tket2-py/src/circuit/tk2circuit.rs
index 9a1bb283..d824356b 100644
--- a/tket2-py/src/circuit/tk2circuit.rs
+++ b/tket2-py/src/circuit/tk2circuit.rs
@@ -15,8 +15,8 @@ use itertools::Itertools;
 use pyo3::exceptions::{PyAttributeError, PyValueError};
 use pyo3::types::{PyAnyMethods, PyModule, PyString, PyTypeMethods};
 use pyo3::{
-    pyclass, pymethods, Bound, FromPyObject, PyAny, PyErr, PyObject, PyRef, PyRefMut, PyResult,
-    PyTypeInfo, Python, ToPyObject,
+    pyclass, pymethods, Bound, FromPyObject, IntoPyObject, PyAny, PyErr, PyObject, PyRef, PyRefMut,
+    PyResult, PyTypeInfo, Python,
 };
 
 use derive_more::From;
@@ -177,9 +177,7 @@ impl Tk2Circuit {
             };
             let tk2_py_op = PyTk2Op::from(tk2_op);
             let cost = cost_fn.call1((tk2_py_op,))?;
-            Ok(PyCircuitCost {
-                cost: cost.to_object(py),
-            })
+            Ok(PyCircuitCost { cost: cost.into() })
         };
         let circ_cost = self.circ.circuit_cost(cost_fn)?;
         Ok(circ_cost.cost.into_bound(py))
diff --git a/tket2-py/src/lib.rs b/tket2-py/src/lib.rs
index 1ebf3969..d86ec71b 100644
--- a/tket2-py/src/lib.rs
+++ b/tket2-py/src/lib.rs
@@ -32,7 +32,7 @@ fn add_submodule(py: Python, parent: &Bound<PyModule>, submodule: Bound<PyModule
     // See [https://github.com/PyO3/pyo3/issues/759]
     let parent_name = parent.name()?;
     let submodule_name = submodule.name()?;
-    let modules = py.import_bound("sys")?.getattr("modules")?;
+    let modules = py.import("sys")?.getattr("modules")?;
     modules.set_item(format!("{parent_name}.{submodule_name}"), submodule)?;
     Ok(())
 }
diff --git a/tket2-py/src/ops.rs b/tket2-py/src/ops.rs
index 623ebced..48649da0 100644
--- a/tket2-py/src/ops.rs
+++ b/tket2-py/src/ops.rs
@@ -14,7 +14,7 @@ use crate::types::PyHugrType;
 
 /// The module definition
 pub fn module(py: Python<'_>) -> PyResult<Bound<'_, PyModule>> {
-    let m = PyModule::new_bound(py, "ops")?;
+    let m = PyModule::new(py, "ops")?;
     m.add_class::<PyTk2Op>()?;
     m.add_class::<PyPauli>()?;
     m.add_class::<PyExtensionOp>()?;
diff --git a/tket2-py/src/optimiser.rs b/tket2-py/src/optimiser.rs
index a3005dc6..345a7545 100644
--- a/tket2-py/src/optimiser.rs
+++ b/tket2-py/src/optimiser.rs
@@ -13,7 +13,7 @@ use crate::circuit::update_circ;
 
 /// The module definition
 pub fn module(py: Python<'_>) -> PyResult<Bound<'_, PyModule>> {
-    let m = PyModule::new_bound(py, "optimiser")?;
+    let m = PyModule::new(py, "optimiser")?;
     m.add_class::<PyBadgerOptimiser>()?;
     Ok(m)
 }
diff --git a/tket2-py/src/passes.rs b/tket2-py/src/passes.rs
index c33fce64..eb7edb5f 100644
--- a/tket2-py/src/passes.rs
+++ b/tket2-py/src/passes.rs
@@ -20,16 +20,13 @@ use crate::{
 ///
 /// This module is re-exported from the python module with the same name.
 pub fn module(py: Python<'_>) -> PyResult<Bound<'_, PyModule>> {
-    let m = PyModule::new_bound(py, "passes")?;
+    let m = PyModule::new(py, "passes")?;
     m.add_function(wrap_pyfunction!(greedy_depth_reduce, &m)?)?;
     m.add_function(wrap_pyfunction!(lower_to_pytket, &m)?)?;
     m.add_function(wrap_pyfunction!(badger_optimise, &m)?)?;
     m.add_class::<self::chunks::PyCircuitChunks>()?;
     m.add_function(wrap_pyfunction!(self::chunks::chunks, &m)?)?;
-    m.add(
-        "PullForwardError",
-        py.get_type_bound::<PyPullForwardError>(),
-    )?;
+    m.add("PullForwardError", py.get_type::<PyPullForwardError>())?;
     Ok(m)
 }
 
@@ -66,11 +63,11 @@ fn greedy_depth_reduce<'py>(circ: &Bound<'py, PyAny>) -> PyResult<(Bound<'py, Py
 fn rebase_nam(circ: &Bound<PyAny>) -> PyResult<()> {
     let py = circ.py();
     let auto_rebase = py
-        .import_bound("pytket.passes.auto_rebase")?
+        .import("pytket.passes.auto_rebase")?
         .getattr("auto_rebase_pass")?;
-    let optype = py.import_bound("pytket")?.getattr("OpType")?;
-    let locals = [("OpType", &optype)].into_py_dict_bound(py);
-    let op_set = py.eval_bound("{OpType.CX, OpType.Rz, OpType.H}", None, Some(&locals))?;
+    let optype = py.import("pytket")?.getattr("OpType")?;
+    let locals = [("OpType", &optype)].into_py_dict(py)?;
+    let op_set = py.eval(c"{OpType.CX, OpType.Rz, OpType.H}", None, Some(&locals))?;
     let rebase_pass = auto_rebase.call1((op_set,))?.getattr("apply")?;
     rebase_pass.call1((circ,)).map(|_| ())
 }
diff --git a/tket2-py/src/pattern.rs b/tket2-py/src/pattern.rs
index 7ffa40be..4afb8520 100644
--- a/tket2-py/src/pattern.rs
+++ b/tket2-py/src/pattern.rs
@@ -13,7 +13,7 @@ use tket2::Circuit;
 
 /// The module definition
 pub fn module(py: Python<'_>) -> PyResult<Bound<'_, PyModule>> {
-    let m = PyModule::new_bound(py, "pattern")?;
+    let m = PyModule::new(py, "pattern")?;
     m.add_class::<Rule>()?;
     m.add_class::<RuleMatcher>()?;
     m.add_class::<self::portmatching::PyCircuitPattern>()?;
@@ -23,11 +23,11 @@ pub fn module(py: Python<'_>) -> PyResult<Bound<'_, PyModule>> {
 
     m.add(
         "InvalidPatternError",
-        py.get_type_bound::<PyInvalidPatternError>(),
+        py.get_type::<PyInvalidPatternError>(),
     )?;
     m.add(
         "InvalidReplacementError",
-        py.get_type_bound::<PyInvalidReplacementError>(),
+        py.get_type::<PyInvalidReplacementError>(),
     )?;
 
     Ok(m)
diff --git a/tket2-py/src/pattern/portmatching.rs b/tket2-py/src/pattern/portmatching.rs
index 02747884..baae2002 100644
--- a/tket2-py/src/pattern/portmatching.rs
+++ b/tket2-py/src/pattern/portmatching.rs
@@ -64,7 +64,7 @@ impl PyPatternMatcher {
     pub fn py_from_patterns(patterns: &Bound<PyIterator>) -> PyResult<Self> {
         Ok(PatternMatcher::from_patterns(
             patterns
-                .iter()?
+                .try_iter()?
                 .map(|p| {
                     let py_pattern = p?.extract::<PyCircuitPattern>()?;
                     Ok(py_pattern.pattern)
diff --git a/tket2-py/src/rewrite.rs b/tket2-py/src/rewrite.rs
index 18c34b41..24a9c626 100644
--- a/tket2-py/src/rewrite.rs
+++ b/tket2-py/src/rewrite.rs
@@ -10,7 +10,7 @@ use crate::circuit::{PyNode, Tk2Circuit};
 
 /// The module definition
 pub fn module(py: Python<'_>) -> PyResult<Bound<'_, PyModule>> {
-    let m = PyModule::new_bound(py, "rewrite")?;
+    let m = PyModule::new(py, "rewrite")?;
     m.add_class::<PyECCRewriter>()?;
     m.add_class::<PyCircuitRewrite>()?;
     m.add_class::<PySubcircuit>()?;
diff --git a/tket2-py/src/types.rs b/tket2-py/src/types.rs
index 273f58b1..8ee997c0 100644
--- a/tket2-py/src/types.rs
+++ b/tket2-py/src/types.rs
@@ -9,7 +9,7 @@ use std::fmt;
 
 /// The module definition
 pub fn module(py: Python<'_>) -> PyResult<Bound<'_, PyModule>> {
-    let m = PyModule::new_bound(py, "types")?;
+    let m = PyModule::new(py, "types")?;
     m.add_class::<PyHugrType>()?;
     m.add_class::<PyTypeBound>()?;
 
diff --git a/tket2/src/serialize/pytket.rs b/tket2/src/serialize/pytket.rs
index 9013f77c..ad117d27 100644
--- a/tket2/src/serialize/pytket.rs
+++ b/tket2/src/serialize/pytket.rs
@@ -23,8 +23,9 @@ use std::{fs, io};
 use hugr::ops::{NamedOp, OpType};
 
 use derive_more::{Display, Error, From};
-use tket_json_rs::circuit_json::{self, SerialCircuit};
+use tket_json_rs::circuit_json::SerialCircuit;
 use tket_json_rs::optype::OpType as SerialOpType;
+use tket_json_rs::register::{Bit, ElementId, Qubit};
 
 use crate::circuit::Circuit;
 
@@ -244,7 +245,7 @@ pub enum OpConvertError {
         /// The expected number of bits.
         expected_bits: usize,
         /// The given of parameters.
-        args: Vec<circuit_json::Register>,
+        args: Vec<ElementId>,
     },
 }
 
@@ -290,8 +291,28 @@ struct RegisterHash {
     hash: u64,
 }
 
-impl From<&circuit_json::Register> for RegisterHash {
-    fn from(reg: &circuit_json::Register) -> Self {
+impl From<&ElementId> for RegisterHash {
+    fn from(reg: &ElementId) -> Self {
+        let mut hasher = DefaultHasher::new();
+        reg.hash(&mut hasher);
+        Self {
+            hash: hasher.finish(),
+        }
+    }
+}
+
+impl From<&Qubit> for RegisterHash {
+    fn from(reg: &Qubit) -> Self {
+        let mut hasher = DefaultHasher::new();
+        reg.hash(&mut hasher);
+        Self {
+            hash: hasher.finish(),
+        }
+    }
+}
+
+impl From<&Bit> for RegisterHash {
+    fn from(reg: &Bit) -> Self {
         let mut hasher = DefaultHasher::new();
         reg.hash(&mut hasher);
         Self {
diff --git a/tket2/src/serialize/pytket/decoder.rs b/tket2/src/serialize/pytket/decoder.rs
index 97cd7fc7..f4e46f40 100644
--- a/tket2/src/serialize/pytket/decoder.rs
+++ b/tket2/src/serialize/pytket/decoder.rs
@@ -17,6 +17,7 @@ use itertools::{EitherOrBoth, Itertools};
 use serde_json::json;
 use tket_json_rs::circuit_json;
 use tket_json_rs::circuit_json::SerialCircuit;
+use tket_json_rs::register;
 
 use super::op::Tk1Op;
 use super::param::decode::{parse_pytket_param, PytketParam};
@@ -80,18 +81,18 @@ impl Tk1Decoder {
         // named 2, at position 1 the register originally named 0, and so on.
         let mut output_qubits = Vec::with_capacity(serialcirc.qubits.len());
         let mut output_bits = Vec::with_capacity(serialcirc.bits.len());
-        let output_to_input: HashMap<circuit_json::Register, circuit_json::Register> = serialcirc
+        let output_to_input: HashMap<register::ElementId, register::ElementId> = serialcirc
             .implicit_permutation
             .iter()
-            .map(|p| (p.1.clone(), p.0.clone()))
+            .map(|p| (p.1.clone().id, p.0.clone().id))
             .collect();
         for qubit in &serialcirc.qubits {
             // For each output position, find the input register that should be there.
-            output_qubits.push(output_to_input.get(qubit).unwrap_or(qubit).clone());
+            output_qubits.push(output_to_input.get(&qubit.id).unwrap_or(&qubit.id).clone());
         }
         for bit in &serialcirc.bits {
             // For each output position, find the input register that should be there.
-            output_bits.push(output_to_input.get(bit).unwrap_or(bit).clone());
+            output_bits.push(output_to_input.get(&bit.id).unwrap_or(&bit.id).clone());
         }
         dfg.set_metadata(METADATA_Q_OUTPUT_REGISTERS, json!(output_qubits));
         dfg.set_metadata(METADATA_B_OUTPUT_REGISTERS, json!(output_bits));
@@ -101,7 +102,8 @@ impl Tk1Decoder {
         let ordered_registers = serialcirc
             .qubits
             .iter()
-            .chain(&serialcirc.bits)
+            .map(|qb| &qb.id)
+            .chain(serialcirc.bits.iter().map(|bit| &bit.id))
             .map(|reg| {
                 check_register(reg)?;
                 Ok(RegisterHash::from(reg))
@@ -192,7 +194,7 @@ impl Tk1Decoder {
     fn get_op_wires(
         &mut self,
         tk1op: &Tk1Op,
-        args: &[circuit_json::Register],
+        args: &[register::ElementId],
         params: Vec<String>,
     ) -> Result<(Vec<Wire>, Vec<RegisterHash>), OpConvertError> {
         // Arguments are always ordered with qubits first, and then bits.
@@ -343,7 +345,7 @@ impl Tk1Decoder {
 }
 
 /// Only single-indexed registers are supported.
-fn check_register(register: &circuit_json::Register) -> Result<(), TK1ConvertError> {
+fn check_register(register: &register::ElementId) -> Result<(), TK1ConvertError> {
     if register.1.len() != 1 {
         Err(TK1ConvertError::MultiIndexedRegister {
             register: register.0.clone(),
diff --git a/tket2/src/serialize/pytket/encoder.rs b/tket2/src/serialize/pytket/encoder.rs
index e0258871..9cae5b27 100644
--- a/tket2/src/serialize/pytket/encoder.rs
+++ b/tket2/src/serialize/pytket/encoder.rs
@@ -9,8 +9,8 @@ use hugr::std_extensions::arithmetic::float_types::FLOAT64_TYPE;
 use hugr::types::Type;
 use hugr::{HugrView, Wire};
 use itertools::Itertools;
-use tket_json_rs::circuit_json::Register as RegisterUnit;
 use tket_json_rs::circuit_json::{self, SerialCircuit};
+use tket_json_rs::register::ElementId as RegisterUnit;
 
 use crate::circuit::command::{CircuitUnit, Command};
 use crate::circuit::Circuit;
@@ -221,15 +221,14 @@ impl Tk1Encoder {
         let mut implicit_permutation = qubits_permutation;
         implicit_permutation.append(&mut bits_permutation);
 
-        SerialCircuit {
-            name: self.name,
-            phase: self.phase,
-            commands: self.commands,
-            qubits,
-            bits,
-            implicit_permutation,
-            number_of_ws: None,
-        }
+        let mut ser = SerialCircuit::new(self.name, self.phase);
+
+        ser.commands = self.commands;
+        ser.qubits = qubits.into_iter().map_into().collect();
+        ser.bits = bits.into_iter().map_into().collect();
+        ser.implicit_permutation = implicit_permutation;
+        ser.number_of_ws = None;
+        ser
     }
 
     /// Translate a linear [`CircuitUnit`] into a [`RegisterUnit`], if possible.
@@ -355,7 +354,7 @@ impl QubitTracker {
         let permutation = outputs
             .into_iter()
             .zip(&self.inputs)
-            .map(|(out, inp)| circuit_json::ImplicitPermutation(inp.clone(), out))
+            .map(|(out, inp)| circuit_json::ImplicitPermutation(inp.clone().into(), out.into()))
             .collect_vec();
 
         (self.inputs, permutation)
@@ -535,7 +534,10 @@ impl BitTracker {
         let permutation = original_permutation
             .into_iter()
             .map(|(inp, out)| {
-                circuit_json::ImplicitPermutation(inp, circuit_permutation.remove(&out).unwrap())
+                circuit_json::ImplicitPermutation(
+                    inp.into(),
+                    circuit_permutation.remove(&out).unwrap().into(),
+                )
             })
             .collect_vec();
 
diff --git a/tket2/src/serialize/pytket/tests.rs b/tket2/src/serialize/pytket/tests.rs
index 37d37f58..ce5ceb00 100644
--- a/tket2/src/serialize/pytket/tests.rs
+++ b/tket2/src/serialize/pytket/tests.rs
@@ -13,6 +13,7 @@ use hugr::HugrView;
 use rstest::{fixture, rstest};
 use tket_json_rs::circuit_json::{self, SerialCircuit};
 use tket_json_rs::optype;
+use tket_json_rs::register;
 
 use super::{TKETDecode, METADATA_INPUT_PARAMETERS, METADATA_Q_OUTPUT_REGISTERS};
 use crate::circuit::Circuit;
@@ -77,21 +78,24 @@ fn validate_serial_circ(circ: &SerialCircuit) {
     for command in &circ.commands {
         for arg in &command.args {
             assert!(
-                circ.qubits.contains(arg) || circ.bits.contains(arg),
+                circ.qubits.contains(&register::Qubit::from(arg.clone()))
+                    || circ.bits.contains(&register::Bit::from(arg.clone())),
                 "Circuit command {command:?} has an invalid argument '{arg:?}'"
             );
         }
     }
 
     // Check that the implicit permutation is valid.
-    let perm: HashMap<circuit_json::Register, circuit_json::Register> = circ
+    let perm: HashMap<register::ElementId, register::ElementId> = circ
         .implicit_permutation
         .iter()
-        .map(|p| (p.0.clone(), p.1.clone()))
+        .map(|p| (p.0.clone().id, p.1.clone().id))
         .collect();
     for (key, value) in &perm {
-        let valid_qubits = circ.qubits.contains(key) && circ.qubits.contains(value);
-        let valid_bits = circ.bits.contains(key) && circ.bits.contains(value);
+        let valid_qubits = circ.qubits.contains(&register::Qubit::from(key.clone()))
+            && circ.qubits.contains(&register::Qubit::from(value.clone()));
+        let valid_bits = circ.bits.contains(&register::Bit::from(key.clone()))
+            && circ.bits.contains(&register::Bit::from(value.clone()));
         assert!(
             valid_qubits || valid_bits,
             "Circuit has an invalid permutation '{key:?} -> {value:?}'"
@@ -103,7 +107,7 @@ fn validate_serial_circ(circ: &SerialCircuit) {
         "Circuit has duplicate permutations",
     );
     assert_eq!(
-        HashSet::<&circuit_json::Register>::from_iter(perm.values()).len(),
+        HashSet::<&register::ElementId>::from_iter(perm.values()).len(),
         perm.len(),
         "Circuit has duplicate values in permutations"
     );