diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0667d1fda..f43f010d8 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -45,53 +45,15 @@ repos:
         name: Formatting the pyproject.toml file
         additional_dependencies: ["tox>=4.9"]
 
-  # Automatic source code formatting
-  - repo: https://github.com/psf/black
-    rev: 24.3.0 # Released 2024-03-15
+  # Format and lint using Ruff
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.0
     hooks:
-      - id: black
-        name: Formatting Python scripts according to Black
-        args: [--safe, --quiet]
-
-  # Automatically sort imports
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2 # Released 2023-12-13
-    hooks:
-      - id: isort
-        name: Tidying Python imports via Isort
-        args: [
-            #'-a', 'from __future__ import annotations',        # 3.7-3.11
-            "--rm",
-            "from __future__ import absolute_import", # -3.0
-            "--rm",
-            "from __future__ import division", # -3.0
-            "--rm",
-            "from __future__ import generator_stop", # -3.7
-            "--rm",
-            "from __future__ import generators", # -2.3
-            "--rm",
-            "from __future__ import nested_scopes", # -2.2
-            "--rm",
-            "from __future__ import print_function", # -3.0
-            "--rm",
-            "from __future__ import unicode_literals", # -3.0
-            "--rm",
-            "from __future__ import with_statement", # -2.6
-          ]
-
-  # Linting
-  - repo: https://github.com/PyCQA/flake8
-    # Release history: https://flake8.pycqa.org/en/latest/release-notes/index.html
-    rev: 7.0.0 # Released 2024-01-05
-    hooks:
-      - id: flake8
-        name: Running Flake8 linter on Python files
-        additional_dependencies: [
-            # Added Flake8-pyproject plugin for .toml compatibility
-            "Flake8-pyproject==1.2.3", # Released 2023-03-21
-            # flake8-comprehensions URL: https://github.com/adamchainz/flake8-comprehensions
-            "flake8-comprehensions==3.14.0", # Released 2023-07-10
-          ]
+      - id: ruff
+        name: Running Ruff linter
+        args: ["--fix"]
+      - id: ruff-format
+        name: Running Ruff formatter
 
   # Type checking
   - repo: https://github.com/pre-commit/mirrors-mypy
diff --git a/pyproject.toml b/pyproject.toml
index db18f1c71..835d0b5e1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -121,53 +121,26 @@ zip-safe = false
 [tool.setuptools.packages.find]
 where = ["src", "tests"]
 
-[tool.isort]
-profile = "black"
-
-[tool.flake8]
-# Flake8-pyproject allows TOML file settings to be read into Flake8
-# URL: https://pypi.org/project/Flake8-pyproject/
-select = [
+[tool.ruff]
+line-length = 88
+lint.extend-ignore = ["E203", "E266", "E501", "E731", "E741"]
+lint.select = [
     "C4",
-    "E401",
-    "E711",
-    "E712",
-    "E713",
-    "E714",
-    "E721",
-    "E722",
-    "E901",
-    "F401",
-    "F402",
-    "F403",
-    "F405",
-    "F541",
-    "F631",
-    "F632",
-    "F633",
-    "F811",
-    "F812",
-    "F821",
-    "F822",
-    "F841",
-    "F901",
-    "W191",
-    "W291",
-    "W292",
-    "W293",
-    "W602",
-    "W603",
-    "W604",
-    "W605",
-    "W606",
-]
-ignore = [
-    "E203",
-    "E266",
-    "E501",
-    "W503",
+    "E4", "E7", "E9",
+    "F",
+    "I",
+    "W6",
 ]
-max-line-length = "88"
+fix = true
+
+[tool.ruff.lint.isort]
+known-first-party = ["murfey"]
+combine-as-imports = true
+
+[tool.ruff.format]
+quote-style="double"
+indent-style="space"
+line-ending="auto"
 
 [tool.pyproject-fmt]
 inputs = "pyproject.toml"
diff --git a/src/murfey/cli/generate_route_manifest.py b/src/murfey/cli/generate_route_manifest.py
index bbea95e3d..d0ee1e464 100644
--- a/src/murfey/cli/generate_route_manifest.py
+++ b/src/murfey/cli/generate_route_manifest.py
@@ -68,7 +68,6 @@ def is_implicitly_resolved(value: str) -> bool:
 
 
 def find_routers(name: str) -> dict[str, APIRouter]:
-
     def _extract_routers_from_module(module: ModuleType):
         routers = {}
         for name, obj in inspect.getmembers(module):
@@ -115,7 +114,6 @@ def _extract_routers_from_module(module: ModuleType):
 
 
 def get_route_manifest(routers: dict[str, APIRouter]):
-
     manifest = {}
 
     for router_name, router in routers.items():
diff --git a/src/murfey/cli/inject_spa_processing.py b/src/murfey/cli/inject_spa_processing.py
index 2294835a5..7a7f66bfa 100644
--- a/src/murfey/cli/inject_spa_processing.py
+++ b/src/murfey/cli/inject_spa_processing.py
@@ -173,7 +173,6 @@ def run():
             / str(ppath.stem + "_motion_corrected.mrc")
         )
         if proc_params:
-
             detached_ids = [c.id for c in collected_ids]
 
             if not mrc_out.parent.exists():
diff --git a/src/murfey/cli/spa_ispyb_messages.py b/src/murfey/cli/spa_ispyb_messages.py
index f78388008..640b585fd 100644
--- a/src/murfey/cli/spa_ispyb_messages.py
+++ b/src/murfey/cli/spa_ispyb_messages.py
@@ -14,8 +14,7 @@
     DataCollectionGroup,
     ProcessingJob,
 )
-from sqlmodel import Session as MurfeySession
-from sqlmodel import create_engine, select
+from sqlmodel import Session as MurfeySession, create_engine, select
 
 from murfey.client.contexts.spa import _get_xml_list_index
 from murfey.server.feedback import _murfey_id, _register
diff --git a/src/murfey/cli/transfer.py b/src/murfey/cli/transfer.py
deleted file mode 100644
index d5bd7a503..000000000
--- a/src/murfey/cli/transfer.py
+++ /dev/null
@@ -1,88 +0,0 @@
-from __future__ import annotations
-
-import argparse
-import subprocess
-from pathlib import Path
-from urllib.parse import ParseResult, urlparse
-
-import requests
-from rich.console import Console
-from rich.prompt import Confirm
-
-from murfey.client import read_config
-from murfey.util.api import url_path_for
-from murfey.util.config import MachineConfig
-
-
-def run():
-    config = read_config()
-    known_server = config["Murfey"].get("server", "")
-    instrument_name = config["Murfey"].get("instrument_name", "")
-
-    parser = argparse.ArgumentParser(description="Transfer using a remote rsync daemon")
-
-    parser.add_argument("--source", type=str, default="")
-    parser.add_argument("--destination", "-d", type=str)
-    parser.add_argument("--destination-prefix", type=str, default="data")
-    parser.add_argument("--delete", action="store_true")
-    parser.add_argument(
-        "--server",
-        metavar="HOST:PORT",
-        type=str,
-        help=f"Murfey server to connect to ({known_server})",
-        default=known_server,
-    )
-
-    args = parser.parse_args()
-
-    console = Console()
-    murfey_url: ParseResult = urlparse(args.server, allow_fragments=False)
-
-    machine_data = MachineConfig(
-        requests.get(
-            f"{murfey_url.geturl()}{url_path_for('session_control.router', 'machine_info_by_instrument', instrument_name=instrument_name)}"
-        ).json()
-    )
-    if Path(args.source or ".").resolve() in machine_data.data_directories:
-        console.print("[red]Source directory is the base directory, exiting")
-        return
-
-    cmd = [
-        "rsync",
-        "-iiv",
-        "--times",
-        "--progress",
-        "-o",  # preserve ownership
-        "-p",  # preserve permissions
-    ]
-    if args.delete:
-        cmd.append("--remove-source-files")
-        if Path(args.source or ".").is_file():
-            num_files = 1
-        else:
-            num_files = len(
-                [f for f in Path(args.source or ".").glob("**/*") if f.is_file()]
-            )
-        delete_prompt = Confirm.ask(
-            f"Do you want to remove {num_files} from {args.source or Path('.').resolve()}?"
-        )
-        if not delete_prompt:
-            return
-    console.print(
-        f"Copying {args.source} -> {murfey_url.hostname}::{args.destination_prefix}/{args.destination}"
-    )
-    if Path(args.source or ".").is_file():
-        cmd.extend(
-            [
-                args.source or ".",
-                f"{murfey_url.hostname}::{args.destination_prefix}/{args.destination}",
-            ]
-        )
-    else:
-        cmd.append("-r")
-        cmd.extend(list(Path(args.source or ".").glob("*")))
-        cmd.append(f"{murfey_url.hostname}::{args.destination}")
-
-    result = subprocess.run(cmd)
-    if result.returncode:
-        console.print(f"[red]rsync failed returning code {result.returncode}")
diff --git a/src/murfey/client/contexts/clem.py b/src/murfey/client/contexts/clem.py
index 0c3aa36b2..772c72959 100644
--- a/src/murfey/client/contexts/clem.py
+++ b/src/murfey/client/contexts/clem.py
@@ -65,7 +65,6 @@ def _get_image_elements(root: ET.Element) -> List[ET.Element]:
     def _find_elements_recursively(
         node: ET.Element,
     ) -> Generator[ET.Element, None, None]:
-
         # Find items labelled "Element" under current node
         elem_list = node.findall("./Children/Element")
         if len(elem_list) < 1:  # Try alternative path for top-level of XML tree
@@ -103,7 +102,6 @@ def post_transfer(
         environment: Optional[MurfeyInstanceEnvironment] = None,
         **kwargs,
     ) -> bool:
-
         super().post_transfer(transferred_file, environment=environment, **kwargs)
 
         # Process files generated by "auto-save" acquisition mode
@@ -188,7 +186,6 @@ def post_transfer(
 
             # Process XLIF files
             if transferred_file.suffix == ".xlif":
-
                 # Skip processing of "_histo" histogram XLIF files
                 if transferred_file.stem.endswith("_histo"):
                     logger.debug(
diff --git a/src/murfey/client/tui/progress.py b/src/murfey/client/tui/progress.py
index b1e787632..f23155a49 100644
--- a/src/murfey/client/tui/progress.py
+++ b/src/murfey/client/tui/progress.py
@@ -71,7 +71,6 @@ def _get_pulse_segments(
     def __rich_console__(
         self, console: Console, options: ConsoleOptions
     ) -> RenderResult:
-
         width = min(self.width or options.max_width, options.max_width)
         ascii = options.ascii_only
         if self.pulse:
diff --git a/src/murfey/client/tui/screens.py b/src/murfey/client/tui/screens.py
index 780eadf9d..21af41dd0 100644
--- a/src/murfey/client/tui/screens.py
+++ b/src/murfey/client/tui/screens.py
@@ -193,7 +193,6 @@ def __init__(
         self._context = SPAModularContext
 
     def compose(self):
-
         machine_data = capture_get(
             base_url=str(self.app._environment.url.geturl()),
             router_name="session_control.router",
@@ -1013,7 +1012,7 @@ def compose(self):
                                     name_root += st
                                 if dest_num:
                                     dest = str(
-                                        dest_path.parent / f"{name_root}{dest_num+1}"
+                                        dest_path.parent / f"{name_root}{dest_num + 1}"
                                     )
                                 else:
                                     dest = str(dest_path.parent / f"{name_root}2")
diff --git a/src/murfey/server/api/auth.py b/src/murfey/server/api/auth.py
index add0f8342..a09c7eeac 100644
--- a/src/murfey/server/api/auth.py
+++ b/src/murfey/server/api/auth.py
@@ -23,8 +23,7 @@
 from murfey.server.murfey_db import murfey_db, url
 from murfey.util.api import url_path_for
 from murfey.util.config import get_security_config
-from murfey.util.db import MurfeyUser as User
-from murfey.util.db import Session as MurfeySession
+from murfey.util.db import MurfeyUser as User, Session as MurfeySession
 
 # Set up logger
 logger = getLogger("murfey.server.api.auth")
@@ -147,7 +146,7 @@ def validate_session_against_visit(session_id: int, visit: str):
 
 
 async def validate_instrument_token(
-    token: Annotated[str, Depends(instrument_oauth2_scheme)]
+    token: Annotated[str, Depends(instrument_oauth2_scheme)],
 ):
     """
     Used by the backend routers to check the incoming instrument server token.
@@ -334,7 +333,6 @@ def validate_user(username: str, password: str) -> bool:
 
 
 def create_access_token(data: dict, token: str = "") -> str:
-
     # If authenticating with password, auth URL needs a 'mint_session_token' endpoint
     if security_config.auth_type == "password":
         if auth_url and data.get("session"):
@@ -420,6 +418,6 @@ async def mint_session_token(session_id: MurfeySessionIDFrontend, db=murfey_db):
 
 @router.get("/validate_token")
 async def simple_token_validation(
-    token: Annotated[str, Depends(validate_instrument_token)]
+    token: Annotated[str, Depends(validate_instrument_token)],
 ):
     return {"valid": True}
diff --git a/src/murfey/server/api/bootstrap.py b/src/murfey/server/api/bootstrap.py
index da74d5bd7..42980ba8b 100644
--- a/src/murfey/server/api/bootstrap.py
+++ b/src/murfey/server/api/bootstrap.py
@@ -308,7 +308,7 @@ def parse_cygwin_request(
         raise ValueError(f"{request_path!r} is not a valid request path")
 
     try:
-        url = f'{find_cygwin_mirror()}{quote(request_path, safe="/")}'
+        url = f"{find_cygwin_mirror()}{quote(request_path, safe='/')}"
     except Exception:
         raise HTTPException(
             status_code=503, detail="Could not identify a suitable Cygwin mirror"
@@ -533,7 +533,7 @@ def get_msys2_environment_index(
         raise ValueError(f"{system!r} is not a valid msys2 environment")
 
     # Construct URL to main MSYS repo and get response
-    arch_url = f'{msys2_url}/{quote(system, safe="/")}'
+    arch_url = f"{msys2_url}/{quote(system, safe='/')}"
     response = http_session.get(arch_url)
 
     # Parse and rewrite package index content
@@ -579,7 +579,7 @@ def get_msys2_package_index(
 
     # Construct URL to main MSYS repo and get response
     package_list_url = (
-        f'{msys2_url}/{quote(system, safe="/")}/{quote(environment, safe="/")}'
+        f"{msys2_url}/{quote(system, safe='/')}/{quote(environment, safe='/')}"
     )
     response = http_session.get(package_list_url)
     return Response(
@@ -617,7 +617,7 @@ def get_msys2_package_file(
         raise ValueError(f"{package!r} is not a valid package name")
 
     # Construct URL to main MSYS repo and get response
-    package_url = f'{msys2_url}/{quote(system, safe="/")}/{quote(environment, safe="/")}/{quote(package, safe="/")}'
+    package_url = f"{msys2_url}/{quote(system, safe='/')}/{quote(environment, safe='/')}/{quote(package, safe='/')}"
     response = http_session.get(package_url)
     if response.status_code != 200:
         raise HTTPException(status_code=response.status_code)
diff --git a/src/murfey/server/api/clem.py b/src/murfey/server/api/clem.py
index f4f2060e3..e5fdbe988 100644
--- a/src/murfey/server/api/clem.py
+++ b/src/murfey/server/api/clem.py
@@ -24,8 +24,8 @@
     CLEMImageStack,
     CLEMLIFFile,
     CLEMTIFFFile,
+    Session as MurfeySession,
 )
-from murfey.util.db import Session as MurfeySession
 
 # Set up logger
 logger = getLogger("murfey.server.api.clem")
@@ -409,7 +409,6 @@ def register_clem_metadata(
     associated_stacks: list[Path] = [],
     db: Session = murfey_db,
 ):
-
     # Return database entry if it already exists
     try:
         clem_metadata: CLEMImageMetadata = get_db_entry(
diff --git a/src/murfey/server/api/file_io_frontend.py b/src/murfey/server/api/file_io_frontend.py
index 531fa81c8..0356859b3 100644
--- a/src/murfey/server/api/file_io_frontend.py
+++ b/src/murfey/server/api/file_io_frontend.py
@@ -2,10 +2,14 @@
 
 from fastapi import APIRouter, Depends
 
-from murfey.server.api.auth import MurfeySessionIDFrontend as MurfeySessionID
-from murfey.server.api.auth import validate_token
-from murfey.server.api.file_io_shared import GainReference
-from murfey.server.api.file_io_shared import process_gain as _process_gain
+from murfey.server.api.auth import (
+    MurfeySessionIDFrontend as MurfeySessionID,
+    validate_token,
+)
+from murfey.server.api.file_io_shared import (
+    GainReference,
+    process_gain as _process_gain,
+)
 from murfey.server.murfey_db import murfey_db
 
 logger = getLogger("murfey.server.api.file_io_frontend")
diff --git a/src/murfey/server/api/file_io_instrument.py b/src/murfey/server/api/file_io_instrument.py
index 4ee48dc40..2644b7f89 100644
--- a/src/murfey/server/api/file_io_instrument.py
+++ b/src/murfey/server/api/file_io_instrument.py
@@ -8,10 +8,14 @@
 from sqlmodel import select
 from werkzeug.utils import secure_filename
 
-from murfey.server.api.auth import MurfeySessionIDInstrument as MurfeySessionID
-from murfey.server.api.auth import validate_instrument_token
-from murfey.server.api.file_io_shared import GainReference
-from murfey.server.api.file_io_shared import process_gain as _process_gain
+from murfey.server.api.auth import (
+    MurfeySessionIDInstrument as MurfeySessionID,
+    validate_instrument_token,
+)
+from murfey.server.api.file_io_shared import (
+    GainReference,
+    process_gain as _process_gain,
+)
 from murfey.server.murfey_db import murfey_db
 from murfey.util import sanitise, secure_path
 from murfey.util.config import get_machine_config
diff --git a/src/murfey/server/api/instrument.py b/src/murfey/server/api/instrument.py
index 699dc01c6..018e62490 100644
--- a/src/murfey/server/api/instrument.py
+++ b/src/murfey/server/api/instrument.py
@@ -14,9 +14,9 @@
 from werkzeug.utils import secure_filename
 
 import murfey.server.prometheus as prom
-from murfey.server.api.auth import MurfeyInstrumentNameFrontend as MurfeyInstrumentName
-from murfey.server.api.auth import MurfeySessionIDFrontend as MurfeySessionID
 from murfey.server.api.auth import (
+    MurfeyInstrumentNameFrontend as MurfeyInstrumentName,
+    MurfeySessionIDFrontend as MurfeySessionID,
     create_access_token,
     instrument_server_tokens,
     oauth2_scheme,
diff --git a/src/murfey/server/api/processing_parameters.py b/src/murfey/server/api/processing_parameters.py
index 80061a234..bbc7ab4cc 100644
--- a/src/murfey/server/api/processing_parameters.py
+++ b/src/murfey/server/api/processing_parameters.py
@@ -6,8 +6,10 @@
 from pydantic import BaseModel
 from sqlmodel import Session, select
 
-from murfey.server.api.auth import MurfeySessionIDFrontend as MurfeySessionID
-from murfey.server.api.auth import validate_token
+from murfey.server.api.auth import (
+    MurfeySessionIDFrontend as MurfeySessionID,
+    validate_token,
+)
 from murfey.server.murfey_db import murfey_db
 from murfey.util.db import SessionProcessingParameters
 
diff --git a/src/murfey/server/api/session_control.py b/src/murfey/server/api/session_control.py
index 255cc0246..6316cbcb3 100644
--- a/src/murfey/server/api/session_control.py
+++ b/src/murfey/server/api/session_control.py
@@ -13,23 +13,20 @@
 
 import murfey.server.prometheus as prom
 from murfey.server import _transport_object
-from murfey.server.api.auth import MurfeySessionIDInstrument as MurfeySessionID
-from murfey.server.api.auth import validate_instrument_token
-from murfey.server.api.shared import get_foil_hole as _get_foil_hole
-from murfey.server.api.shared import (
-    get_foil_holes_from_grid_square as _get_foil_holes_from_grid_square,
+from murfey.server.api.auth import (
+    MurfeySessionIDInstrument as MurfeySessionID,
+    validate_instrument_token,
 )
-from murfey.server.api.shared import get_grid_squares as _get_grid_squares
 from murfey.server.api.shared import (
+    get_foil_hole as _get_foil_hole,
+    get_foil_holes_from_grid_square as _get_foil_holes_from_grid_square,
+    get_grid_squares as _get_grid_squares,
     get_grid_squares_from_dcg as _get_grid_squares_from_dcg,
-)
-from murfey.server.api.shared import (
     get_machine_config_for_instrument,
     get_upstream_tiff_dirs,
     remove_session_by_id,
 )
-from murfey.server.ispyb import DB as ispyb_db
-from murfey.server.ispyb import get_all_ongoing_visits
+from murfey.server.ispyb import DB as ispyb_db, get_all_ongoing_visits
 from murfey.server.murfey_db import murfey_db
 from murfey.util import sanitise
 from murfey.util.config import MachineConfig, get_machine_config
@@ -57,8 +54,6 @@
 from murfey.workflows.spa.atlas import atlas_jpg_from_mrc
 from murfey.workflows.spa.flush_spa_preprocess import (
     register_foil_hole as _register_foil_hole,
-)
-from murfey.workflows.spa.flush_spa_preprocess import (
     register_grid_square as _register_grid_square,
 )
 from murfey.workflows.tomo.tomo_metadata import (
diff --git a/src/murfey/server/api/session_info.py b/src/murfey/server/api/session_info.py
index bc6014347..62f3be1f3 100644
--- a/src/murfey/server/api/session_info.py
+++ b/src/murfey/server/api/session_info.py
@@ -12,24 +12,21 @@
 import murfey.server.api.websocket as ws
 from murfey.server import _transport_object
 from murfey.server.api import templates
-from murfey.server.api.auth import MurfeyInstrumentNameFrontend as MurfeyInstrumentName
-from murfey.server.api.auth import MurfeySessionIDFrontend as MurfeySessionID
-from murfey.server.api.auth import validate_token
-from murfey.server.api.shared import get_foil_hole as _get_foil_hole
-from murfey.server.api.shared import (
-    get_foil_holes_from_grid_square as _get_foil_holes_from_grid_square,
+from murfey.server.api.auth import (
+    MurfeyInstrumentNameFrontend as MurfeyInstrumentName,
+    MurfeySessionIDFrontend as MurfeySessionID,
+    validate_token,
 )
-from murfey.server.api.shared import get_grid_squares as _get_grid_squares
 from murfey.server.api.shared import (
+    get_foil_hole as _get_foil_hole,
+    get_foil_holes_from_grid_square as _get_foil_holes_from_grid_square,
+    get_grid_squares as _get_grid_squares,
     get_grid_squares_from_dcg as _get_grid_squares_from_dcg,
-)
-from murfey.server.api.shared import (
     get_machine_config_for_instrument,
     get_upstream_tiff_dirs,
     remove_session_by_id,
 )
-from murfey.server.ispyb import DB as ispyb_db
-from murfey.server.ispyb import get_all_ongoing_visits
+from murfey.server.ispyb import DB as ispyb_db, get_all_ongoing_visits
 from murfey.server.murfey_db import murfey_db
 from murfey.util import sanitise
 from murfey.util.config import MachineConfig, get_machine_config
diff --git a/src/murfey/server/api/workflow.py b/src/murfey/server/api/workflow.py
index dcfbea914..8fec45f5d 100644
--- a/src/murfey/server/api/workflow.py
+++ b/src/murfey/server/api/workflow.py
@@ -26,8 +26,10 @@
 
 import murfey.server.prometheus as prom
 from murfey.server import _transport_object
-from murfey.server.api.auth import MurfeySessionIDInstrument as MurfeySessionID
-from murfey.server.api.auth import validate_instrument_token
+from murfey.server.api.auth import (
+    MurfeySessionIDInstrument as MurfeySessionID,
+    validate_instrument_token,
+)
 from murfey.server.feedback import (
     _murfey_id,
     check_tilt_series_mc,
@@ -36,8 +38,7 @@
     get_job_ids,
     get_tomo_proc_params,
 )
-from murfey.server.ispyb import DB as ispyb_db
-from murfey.server.ispyb import get_proposal_id
+from murfey.server.ispyb import DB as ispyb_db, get_proposal_id
 from murfey.server.murfey_db import murfey_db
 from murfey.util import sanitise
 from murfey.util.config import get_machine_config
@@ -435,7 +436,6 @@ async def request_spa_preprocessing(
         )
         foil_hole_id = None
     if proc_params:
-
         detached_ids = [c.id for c in collected_ids]
 
         murfey_ids = _murfey_id(detached_ids[3], db, number=2, close=False)
@@ -494,9 +494,9 @@ async def request_spa_preprocessing(
         }
         # log.info(f"Sending Zocalo message {zocalo_message}")
         if _transport_object:
-            zocalo_message["parameters"][
-                "feedback_queue"
-            ] = _transport_object.feedback_queue
+            zocalo_message["parameters"]["feedback_queue"] = (
+                _transport_object.feedback_queue
+            )
             _transport_object.send("processing_recipe", zocalo_message)
         else:
             logger.error(
@@ -723,9 +723,9 @@ async def request_tomography_preprocessing(
             },
         }
         if _transport_object:
-            zocalo_message["parameters"][
-                "feedback_queue"
-            ] = _transport_object.feedback_queue
+            zocalo_message["parameters"]["feedback_queue"] = (
+                _transport_object.feedback_queue
+            )
             _transport_object.send("processing_recipe", zocalo_message)
         else:
             logger.error(
diff --git a/src/murfey/server/demo_api.py b/src/murfey/server/demo_api.py
index 24280d5de..c59cde2c3 100644
--- a/src/murfey/server/demo_api.py
+++ b/src/murfey/server/demo_api.py
@@ -22,8 +22,10 @@
 import murfey.server.api.bootstrap
 import murfey.server.prometheus as prom
 from murfey.server.api import templates
-from murfey.server.api.auth import MurfeySessionIDFrontend as MurfeySessionID
-from murfey.server.api.auth import validate_token
+from murfey.server.api.auth import (
+    MurfeySessionIDFrontend as MurfeySessionID,
+    validate_token,
+)
 from murfey.server.api.session_info import Visit
 from murfey.server.api.workflow import (
     DCGroupParameters,
diff --git a/src/murfey/server/feedback.py b/src/murfey/server/feedback.py
index fd5a68207..288f3926f 100644
--- a/src/murfey/server/feedback.py
+++ b/src/murfey/server/feedback.py
@@ -390,9 +390,9 @@ def _release_2d_hold(message: dict, _db):
         _db.commit()
         _db.close()
         if murfey.server._transport_object:
-            zocalo_message["parameters"][
-                "feedback_queue"
-            ] = murfey.server._transport_object.feedback_queue
+            zocalo_message["parameters"]["feedback_queue"] = (
+                murfey.server._transport_object.feedback_queue
+            )
             murfey.server._transport_object.send(
                 "processing_recipe", zocalo_message, new_connection=True
             )
@@ -466,9 +466,9 @@ def _release_3d_hold(message: dict, _db):
             "recipes": ["em-spa-class3d"],
         }
         if murfey.server._transport_object:
-            zocalo_message["parameters"][
-                "feedback_queue"
-            ] = murfey.server._transport_object.feedback_queue
+            zocalo_message["parameters"]["feedback_queue"] = (
+                murfey.server._transport_object.feedback_queue
+            )
             murfey.server._transport_object.send(
                 "processing_recipe", zocalo_message, new_connection=True
             )
@@ -547,9 +547,9 @@ def _release_refine_hold(message: dict, _db):
             "recipes": ["em-spa-refine"],
         }
         if murfey.server._transport_object:
-            zocalo_message["parameters"][
-                "feedback_queue"
-            ] = murfey.server._transport_object.feedback_queue
+            zocalo_message["parameters"]["feedback_queue"] = (
+                murfey.server._transport_object.feedback_queue
+            )
             murfey.server._transport_object.send(
                 "processing_recipe", zocalo_message, new_connection=True
             )
@@ -662,9 +662,9 @@ def _register_incomplete_2d_batch(message: dict, _db, demo: bool = False):
         "recipes": ["em-spa-class2d"],
     }
     if murfey.server._transport_object:
-        zocalo_message["parameters"][
-            "feedback_queue"
-        ] = murfey.server._transport_object.feedback_queue
+        zocalo_message["parameters"]["feedback_queue"] = (
+            murfey.server._transport_object.feedback_queue
+        )
         murfey.server._transport_object.send(
             "processing_recipe", zocalo_message, new_connection=True
         )
@@ -825,9 +825,9 @@ def _register_complete_2d_batch(message: dict, _db, demo: bool = False):
             "recipes": ["em-spa-class2d"],
         }
         if murfey.server._transport_object:
-            zocalo_message["parameters"][
-                "feedback_queue"
-            ] = murfey.server._transport_object.feedback_queue
+            zocalo_message["parameters"]["feedback_queue"] = (
+                murfey.server._transport_object.feedback_queue
+            )
             murfey.server._transport_object.send(
                 "processing_recipe", zocalo_message, new_connection=True
             )
@@ -894,9 +894,9 @@ def _register_complete_2d_batch(message: dict, _db, demo: bool = False):
             "recipes": ["em-spa-class2d"],
         }
         if murfey.server._transport_object:
-            zocalo_message["parameters"][
-                "feedback_queue"
-            ] = murfey.server._transport_object.feedback_queue
+            zocalo_message["parameters"]["feedback_queue"] = (
+                murfey.server._transport_object.feedback_queue
+            )
             murfey.server._transport_object.send(
                 "processing_recipe", zocalo_message, new_connection=True
             )
@@ -984,9 +984,9 @@ def _flush_class2d(
             "recipes": ["em-spa-class2d"],
         }
         if murfey.server._transport_object:
-            zocalo_message["parameters"][
-                "feedback_queue"
-            ] = murfey.server._transport_object.feedback_queue
+            zocalo_message["parameters"]["feedback_queue"] = (
+                murfey.server._transport_object.feedback_queue
+            )
             murfey.server._transport_object.send(
                 "processing_recipe", zocalo_message, new_connection=True
             )
@@ -1266,7 +1266,7 @@ def _register_3d_batch(message: dict, _db, demo: bool = False):
             other_options["initial_model"] = str(rescaled_initial_model_path)
             next_job = feedback_params.next_job
             class3d_dir = (
-                f"{class3d_message['class3d_dir']}{(feedback_params.next_job+1):03}"
+                f"{class3d_message['class3d_dir']}{(feedback_params.next_job + 1):03}"
             )
             feedback_params.next_job += 1
             _db.add(feedback_params)
@@ -1305,7 +1305,7 @@ def _register_3d_batch(message: dict, _db, demo: bool = False):
         # For the first batch, start a container and set the database to wait
         next_job = feedback_params.next_job
         class3d_dir = (
-            f"{class3d_message['class3d_dir']}{(feedback_params.next_job+1):03}"
+            f"{class3d_message['class3d_dir']}{(feedback_params.next_job + 1):03}"
         )
         class3d_grp_uuid = _murfey_id(message["program_id"], _db)[0]
         class_uuids = _murfey_id(message["program_id"], _db, number=4)
@@ -1351,9 +1351,9 @@ def _register_3d_batch(message: dict, _db, demo: bool = False):
             "recipes": ["em-spa-class3d"],
         }
         if murfey.server._transport_object:
-            zocalo_message["parameters"][
-                "feedback_queue"
-            ] = murfey.server._transport_object.feedback_queue
+            zocalo_message["parameters"]["feedback_queue"] = (
+                murfey.server._transport_object.feedback_queue
+            )
             murfey.server._transport_object.send(
                 "processing_recipe", zocalo_message, new_connection=True
             )
@@ -1394,9 +1394,9 @@ def _register_3d_batch(message: dict, _db, demo: bool = False):
             "recipes": ["em-spa-class3d"],
         }
         if murfey.server._transport_object:
-            zocalo_message["parameters"][
-                "feedback_queue"
-            ] = murfey.server._transport_object.feedback_queue
+            zocalo_message["parameters"]["feedback_queue"] = (
+                murfey.server._transport_object.feedback_queue
+            )
             murfey.server._transport_object.send(
                 "processing_recipe", zocalo_message, new_connection=True
             )
@@ -1512,9 +1512,9 @@ def _flush_tomography_preprocessing(message: dict, _db):
             f"Launching tomography preprocessing with Zocalo message: {zocalo_message}"
         )
         if murfey.server._transport_object:
-            zocalo_message["parameters"][
-                "feedback_queue"
-            ] = murfey.server._transport_object.feedback_queue
+            zocalo_message["parameters"]["feedback_queue"] = (
+                murfey.server._transport_object.feedback_queue
+            )
             murfey.server._transport_object.send(
                 "processing_recipe", zocalo_message, new_connection=True
             )
@@ -1695,9 +1695,9 @@ def _register_refinement(message: dict, _db, demo: bool = False):
             "recipes": ["em-spa-refine"],
         }
         if murfey.server._transport_object:
-            zocalo_message["parameters"][
-                "feedback_queue"
-            ] = murfey.server._transport_object.feedback_queue
+            zocalo_message["parameters"]["feedback_queue"] = (
+                murfey.server._transport_object.feedback_queue
+            )
             murfey.server._transport_object.send(
                 "processing_recipe", zocalo_message, new_connection=True
             )
@@ -1818,9 +1818,9 @@ def _register_bfactors(message: dict, _db, demo: bool = False):
             "recipes": ["em-spa-bfactor"],
         }
         if murfey.server._transport_object:
-            zocalo_message["parameters"][
-                "feedback_queue"
-            ] = murfey.server._transport_object.feedback_queue
+            zocalo_message["parameters"]["feedback_queue"] = (
+                murfey.server._transport_object.feedback_queue
+            )
             murfey.server._transport_object.send(
                 "processing_recipe", zocalo_message, new_connection=True
             )
diff --git a/src/murfey/server/ispyb.py b/src/murfey/server/ispyb.py
index a09220dcc..70dc58e8c 100644
--- a/src/murfey/server/ispyb.py
+++ b/src/murfey/server/ispyb.py
@@ -706,7 +706,6 @@ def get_session_id(
     visit_number: str,
     db: Session | None,
 ) -> int | None:
-
     # Log received lookup parameters
     log.debug(
         "Looking up ISPyB BLSession ID using the following values:\n"
diff --git a/src/murfey/util/client.py b/src/murfey/util/client.py
index 1b1119aea..c7d897a79 100644
--- a/src/murfey/util/client.py
+++ b/src/murfey/util/client.py
@@ -232,7 +232,9 @@ async def anotify(
         listeners = (
             self._secondary_listeners
             if secondary
-            else self._final_listeners if final else self._listeners
+            else self._final_listeners
+            if final
+            else self._listeners
         )
         for notify_function in listeners:
             result = notify_function(*args, **kwargs)
@@ -253,7 +255,9 @@ def notify(
         listeners = (
             self._secondary_listeners
             if secondary
-            else self._final_listeners if final else self._listeners
+            else self._final_listeners
+            if final
+            else self._listeners
         )
         for notify_function in listeners:
             result = notify_function(*args, **kwargs)
diff --git a/src/murfey/util/db.py b/src/murfey/util/db.py
index 8dee78fcf..ef1606130 100644
--- a/src/murfey/util/db.py
+++ b/src/murfey/util/db.py
@@ -195,7 +195,6 @@ class CLEMTIFFFile(SQLModel, table=True):  # type: ignore
 
 
 class CLEMImageMetadata(SQLModel, table=True):  # type: ignore
-
     id: Optional[int] = Field(default=None, primary_key=True)
     file_path: str = Field(index=True)  # Full path to metadata file
 
diff --git a/src/murfey/util/spa_metadata.py b/src/murfey/util/spa_metadata.py
index e471aa93d..2a11ffebf 100644
--- a/src/murfey/util/spa_metadata.py
+++ b/src/murfey/util/spa_metadata.py
@@ -49,7 +49,9 @@ def foil_hole_from_file(f: Path) -> int:
     return int(f.name.split("_")[1])
 
 
-def get_grid_square_atlas_positions(xml_path: Path, grid_square: str = "") -> Dict[
+def get_grid_square_atlas_positions(
+    xml_path: Path, grid_square: str = ""
+) -> Dict[
     str,
     Tuple[
         Optional[int],
diff --git a/src/murfey/workflows/clem/__init__.py b/src/murfey/workflows/clem/__init__.py
index 16ff4e4f7..b40d48cb3 100644
--- a/src/murfey/workflows/clem/__init__.py
+++ b/src/murfey/workflows/clem/__init__.py
@@ -15,8 +15,8 @@
     CLEMImageStack,
     CLEMLIFFile,
     CLEMTIFFFile,
+    Session as MurfeySession,
 )
-from murfey.util.db import Session as MurfeySession
 
 logger = logging.getLogger("murfey.workflows.clem")
 
diff --git a/src/murfey/workflows/clem/register_preprocessing_results.py b/src/murfey/workflows/clem/register_preprocessing_results.py
index 191512c1c..f52ccb471 100644
--- a/src/murfey/workflows/clem/register_preprocessing_results.py
+++ b/src/murfey/workflows/clem/register_preprocessing_results.py
@@ -24,8 +24,8 @@
     CLEMImageStack,
     CLEMLIFFile,
     CLEMTIFFFile,
+    Session as MurfeySession,
 )
-from murfey.util.db import Session as MurfeySession
 from murfey.util.processing_params import (
     default_clem_align_and_merge_parameters as processing_params,
 )
@@ -57,7 +57,6 @@ class CLEMPreprocessingResult(BaseModel):
 
 
 def run(message: dict, murfey_db: Session, demo: bool = False) -> bool:
-
     session_id: int = (
         int(message["session_id"])
         if not isinstance(message["session_id"], int)
diff --git a/src/murfey/workflows/spa/flush_spa_preprocess.py b/src/murfey/workflows/spa/flush_spa_preprocess.py
index b225dfb69..98dc83096 100644
--- a/src/murfey/workflows/spa/flush_spa_preprocess.py
+++ b/src/murfey/workflows/spa/flush_spa_preprocess.py
@@ -20,9 +20,10 @@
     Movie,
     PreprocessStash,
     ProcessingJob,
+    Session as MurfeySession,
+    SPAFeedbackParameters,
+    SPARelionParameters,
 )
-from murfey.util.db import Session as MurfeySession
-from murfey.util.db import SPAFeedbackParameters, SPARelionParameters
 from murfey.util.models import FoilHoleParameters, GridSquareParameters
 from murfey.util.processing_params import cryolo_model_path, default_spa_parameters
 from murfey.util.spa_metadata import (
@@ -430,9 +431,9 @@ def flush_spa_preprocess(message: dict, murfey_db: Session, demo: bool = False)
             },
         }
         if _transport_object:
-            zocalo_message["parameters"][
-                "feedback_queue"
-            ] = _transport_object.feedback_queue
+            zocalo_message["parameters"]["feedback_queue"] = (
+                _transport_object.feedback_queue
+            )
             _transport_object.send(
                 "processing_recipe", zocalo_message, new_connection=True
             )
diff --git a/src/murfey/workflows/spa/picking.py b/src/murfey/workflows/spa/picking.py
index e383f438f..72a1e3ba2 100644
--- a/src/murfey/workflows/spa/picking.py
+++ b/src/murfey/workflows/spa/picking.py
@@ -25,9 +25,10 @@
     ParticleSizes,
     ProcessingJob,
     SelectionStash,
+    Session as MurfeySession,
+    SPAFeedbackParameters,
+    SPARelionParameters,
 )
-from murfey.util.db import Session as MurfeySession
-from murfey.util.db import SPAFeedbackParameters, SPARelionParameters
 from murfey.util.processing_params import default_spa_parameters
 
 logger = getLogger("murfey.workflows.spa.picking")
@@ -154,9 +155,9 @@ def _register_picked_particles_use_diameter(
                     "recipes": ["em-spa-extract"],
                 }
                 if _transport_object:
-                    zocalo_message["parameters"][
-                        "feedback_queue"
-                    ] = _transport_object.feedback_queue
+                    zocalo_message["parameters"]["feedback_queue"] = (
+                        _transport_object.feedback_queue
+                    )
                     _transport_object.send(
                         "processing_recipe", zocalo_message, new_connection=True
                     )
@@ -194,9 +195,9 @@ def _register_picked_particles_use_diameter(
                 "recipes": ["em-spa-extract"],
             }
             if _transport_object:
-                zocalo_message["parameters"][
-                    "feedback_queue"
-                ] = _transport_object.feedback_queue
+                zocalo_message["parameters"]["feedback_queue"] = (
+                    _transport_object.feedback_queue
+                )
                 _transport_object.send(
                     "processing_recipe", zocalo_message, new_connection=True
                 )
@@ -316,9 +317,9 @@ def _register_picked_particles_use_boxsize(message: dict, _db: Session):
         "recipes": ["em-spa-extract"],
     }
     if _transport_object:
-        zocalo_message["parameters"][
-            "feedback_queue"
-        ] = _transport_object.feedback_queue
+        zocalo_message["parameters"]["feedback_queue"] = (
+            _transport_object.feedback_queue
+        )
         _transport_object.send("processing_recipe", zocalo_message, new_connection=True)
     _db.close()
 
diff --git a/src/murfey/workflows/tomo/tomo_metadata.py b/src/murfey/workflows/tomo/tomo_metadata.py
index 9c145ab6a..2dbc25cb7 100644
--- a/src/murfey/workflows/tomo/tomo_metadata.py
+++ b/src/murfey/workflows/tomo/tomo_metadata.py
@@ -8,9 +8,12 @@
 from murfey.server.gain import Camera
 from murfey.util import sanitise
 from murfey.util.config import get_machine_config
-from murfey.util.db import DataCollectionGroup, SearchMap
-from murfey.util.db import Session as MurfeySession
-from murfey.util.db import TiltSeries
+from murfey.util.db import (
+    DataCollectionGroup,
+    SearchMap,
+    Session as MurfeySession,
+    TiltSeries,
+)
 from murfey.util.models import BatchPositionParameters, SearchMapParameters
 
 logger = logging.getLogger("murfey.client.util.tomo_metadata")
diff --git a/tests/conftest.py b/tests/conftest.py
index 247744512..4429e6074 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -12,10 +12,8 @@
 from sqlalchemy import Engine, RootTransaction, and_, create_engine, event, select
 from sqlalchemy.exc import InterfaceError
 from sqlalchemy.ext.declarative import DeclarativeMeta
-from sqlalchemy.orm import Session as SQLAlchemySession
-from sqlalchemy.orm import sessionmaker
-from sqlmodel import Session as SQLModelSession
-from sqlmodel import SQLModel
+from sqlalchemy.orm import Session as SQLAlchemySession, sessionmaker
+from sqlmodel import Session as SQLModelSession, SQLModel
 
 from murfey.util.db import Session as MurfeySession
 
diff --git a/tests/instrument_server/test_api.py b/tests/instrument_server/test_api.py
index 54ed53563..cf48b3ba7 100644
--- a/tests/instrument_server/test_api.py
+++ b/tests/instrument_server/test_api.py
@@ -8,9 +8,11 @@
 from fastapi.testclient import TestClient
 from pytest_mock import MockerFixture
 
-from murfey.instrument_server.api import _get_murfey_url
-from murfey.instrument_server.api import router as client_router
-from murfey.instrument_server.api import validate_session_token
+from murfey.instrument_server.api import (
+    _get_murfey_url,
+    router as client_router,
+    validate_session_token,
+)
 from murfey.util import posix_path
 from murfey.util.api import url_path_for
 
diff --git a/tests/instrument_server/test_init.py b/tests/instrument_server/test_init.py
index 30e218b67..e575ecea0 100644
--- a/tests/instrument_server/test_init.py
+++ b/tests/instrument_server/test_init.py
@@ -12,8 +12,7 @@
 import murfey
 from murfey.client.update import UPDATE_SUCCESS
 from murfey.instrument_server import check_for_updates, start_instrument_server
-from murfey.server.api.bootstrap import pypi as pypi_router
-from murfey.server.api.bootstrap import version as version_router
+from murfey.server.api.bootstrap import pypi as pypi_router, version as version_router
 from murfey.util.api import url_path_for
 
 # Set up a test router with only the essential endpoints
@@ -37,7 +36,6 @@ def test_check_for_updates(
     test_params: tuple[str],
     mocker: MockerFixture,
 ):
-
     # Unpack test params
     (bump_client_version,) = test_params
 
@@ -136,7 +134,6 @@ def test_check_for_updates(
 def test_start_instrument_server(
     mocker: MockerFixture, test_params: tuple[Optional[str], Optional[int]]
 ):
-
     # Unpack test params
     host, port = test_params
 
diff --git a/tests/server/api/test_movies.py b/tests/server/api/test_movies.py
index 00cc4f464..a3c8abe89 100644
--- a/tests/server/api/test_movies.py
+++ b/tests/server/api/test_movies.py
@@ -15,7 +15,6 @@
 def test_movie_count(
     murfey_db_session: Session,  # From conftest.py
 ):
-
     # Insert table dependencies
     dcg_entry: DataCollectionGroup = get_or_create_db_entry(
         murfey_db_session,
diff --git a/tests/workflows/clem/test_align_and_merge.py b/tests/workflows/clem/test_align_and_merge.py
index 96e4cc430..b7d5d8ec3 100644
--- a/tests/workflows/clem/test_align_and_merge.py
+++ b/tests/workflows/clem/test_align_and_merge.py
@@ -1,4 +1,5 @@
 from pathlib import Path
+from typing import Literal
 from unittest.mock import MagicMock, patch
 
 import pytest
@@ -24,9 +25,9 @@
 
 # Align and merge settings
 crop_to_n_frames = 20
-align_self = "enabled"
-flatten = "max"
-align_across = "enabled"
+align_self: Literal["enabled", ""] = "enabled"
+flatten: Literal["mean", "min", "max", ""] = "max"
+align_across: Literal["enabled", ""] = "enabled"
 
 
 @pytest.fixture
@@ -38,7 +39,6 @@ def processed_dir(tmp_path: Path):
 
 @pytest.fixture
 def image_stacks(processed_dir: Path):
-
     image_dir = processed_dir / area_name / series_name
     image_dir.mkdir(parents=True, exist_ok=True)
 
@@ -52,7 +52,6 @@ def image_stacks(processed_dir: Path):
 
 @pytest.fixture
 def metadata(processed_dir: Path):
-
     metadata_dir = processed_dir / area_name / series_name / "metadata"
     metadata_dir.mkdir(parents=True, exist_ok=True)
 
@@ -70,7 +69,6 @@ def test_submit_cluster_request(
     metadata: Path,
     processed_dir: Path,
 ):
-
     # Construct the long series name
     series_name_long = "--".join(
         image_stacks[0].parent.relative_to(processed_dir).parts
diff --git a/tests/workflows/clem/test_process_raw_lifs.py b/tests/workflows/clem/test_process_raw_lifs.py
index 3399a80df..32b573fc8 100644
--- a/tests/workflows/clem/test_process_raw_lifs.py
+++ b/tests/workflows/clem/test_process_raw_lifs.py
@@ -33,7 +33,6 @@ def test_zocalo_cluster_request(
     lif_file: Path,
     raw_dir: Path,
 ):
-
     # Create a mock tranpsort object
     mock_transport = MagicMock(spec=TransportManager)
     mock_transport.feedback_queue = feedback_queue
diff --git a/tests/workflows/clem/test_process_raw_tiffs.py b/tests/workflows/clem/test_process_raw_tiffs.py
index f784a154f..6cc92bcf2 100644
--- a/tests/workflows/clem/test_process_raw_tiffs.py
+++ b/tests/workflows/clem/test_process_raw_tiffs.py
@@ -54,7 +54,6 @@ def test_zocalo_cluster_request(
     metadata: Path,
     raw_dir: Path,
 ):
-
     # Create a mock tranpsort object
     mock_transport = MagicMock(spec=TransportManager)
     mock_transport.feedback_queue = feedback_queue