Tecan Infinite 200 PRO plate reader backend (Infinite M Plex) #797

hazlamshamin · 2025-12-20T10:14:08Z

Add Tecan Infinite 200 PRO backend + tests.
Supports absorbance and fluorescence, including masking to read specified list of wells, up to 384-well plate.
Luminescence is experimental due to lack of glowing sample for testing.
Make USB capture decoding resilient to malformed escape sequences.

EDIT: all three modes now reflect what OEM does with 100% accuracy, and luminescence is no longer experimental ([e92c6db])

Tests: make lint, make format-check, make typecheck, make test.

Copilot

Pull request overview

This PR introduces a backend for the Tecan Infinite 200 PRO plate reader (M Plex series), adding support for absorbance and fluorescence measurements with experimental luminescence support. The implementation includes configurable well masking for reading specific wells on plates up to 384-well format.

Key changes:

New TecanInfinite200ProBackend class with USB communication and measurement decoding
Specialized decoders for absorbance, fluorescence, and luminescence measurement streams
Enhanced USB capture error handling to gracefully manage malformed escape sequences

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 5 comments.

File	Description
pylabrobot/plate_reading/tecan_infinite_backend.py	Implements the complete backend with transport layer, measurement decoders, and plate reading methods for all three modes
pylabrobot/plate_reading/tecan_infinite_backend_tests.py	Comprehensive unit tests for decoders, scan geometry, and ASCII frame handling
pylabrobot/plate_reading/init.py	Exports the new backend and configuration class for public API access
pylabrobot/io/usb.py	Adds error handling to decode operations to prevent crashes from malformed USB data

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pylabrobot/io/usb.py

pylabrobot/plate_reading/tecan_infinite_backend.py

pylabrobot/plate_reading/tecan/infinite_backend.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

rickwierenga

apologies for the late response, I was working on slas and then the old nimbus PR

I have two small initial questions / comments for things I think we can parameterize easily

pylabrobot/plate_reading/tecan/infinite_backend.py

- USB._read_packet() now accepts optional size to read exact bytes from wire - USB.read() passes remaining byte count to _read_packet() when size specified - PyUSBInfiniteTransport.read() uses new size parameter instead of slicing - USBValidator.read() updated for interface consistency Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Remove InfiniteTransport protocol and PyUSBInfiniteTransport class - TecanInfinite200ProBackend creates USB instance internally as self.io - Move reset logic into backend's _recover_transport method - Simplifies the transport layer by removing unnecessary abstraction Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

rickwierenga · 2026-01-21T00:29:50Z

could you please explain what _MODE_CAPABILITY_COMMANDS are?

are they just more parameters like this?

      f"BEAM DIAMETER={self._capability_numeric('ABS', '#BEAM DIAMETER', 700)}",

that we can add as commands? why not add them?

Replace custom _u16be, _u32be, _i32be helper functions with the Reader class from io/binary using little_endian=False for big-endian parsing. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Remove redundant step_loss local variable and parameter since _end_run can access self._active_step_loss_commands directly. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Inline command lists in _configure_absorbance, _configure_fluorescence, and _configure_luminescence with direct _send_ascii calls - Refactor _cleanup_protocol to use a local helper function instead of building a commands list Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Rename: - _send_ascii -> _send_command - _frame_ascii_command -> _frame_command - _drain_ascii -> _drain - _read_ascii_response -> _read_command_response - _ascii_parser -> _parser Also update related docstrings. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Tests verify that open, close, read_absorbance, read_fluorescence, and read_luminescence send the correct USB commands in the correct order. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Reduces duplication across read_absorbance, read_fluorescence, and read_luminescence methods. Also removes unused _active_mode field. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Callers now compute ordered_wells and scan_wells once and pass ordered_wells to _run_scan directly. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

The "Prepare" naming came from the device command "PREPARE REF" but didn't convey what the data actually represents. These structures contain calibration data (dark/bright references, gain values) used to convert raw measurements into calibrated values. Renamed: - _AbsorbancePrepare -> _AbsorbanceCalibration - _FluorescencePrepare -> _FluorescenceCalibration - _LuminescencePrepare -> _LuminescenceCalibration - Related functions, properties, and variables Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Use distinct variable names (cal/data) instead of reusing 'decoded' for both calibration and measurement data decoding to avoid mypy type conflicts. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

The "marker" name was misleading - it's actually the binary payload length extracted from protocol frames like "18,BIN:". The length happens to identify packet type (different packet types have characteristic sizes), but calling it "marker" obscured its true meaning. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

rickwierenga · 2026-01-21T05:09:23Z

pylabrobot/plate_reading/tecan/infinite_backend.py

+  async def _begin_run(self) -> None:
+    await self._initialize_device()
+    self._reset_stream_state()


is there a reason the device would un-initialize? every command calls _begin_run, which calls _initialize_device. but _initialize_device is already called on setup.

Currently, this is the fallback when there is any glitch with the usb. _device_initialized=True and no re-initialisation is being done if the flag remains True. However, I did notice, like sometimes, after leaving the machine for few hours, when I tried to read the plate, the computer fails to connect/control the plate reader (even after I have included this fallback). Still unsure what is the reason for this, that I had to physically power cycle and disconnect-reconnect the usb cable for it to work. Do you have any idea why this happen or what's the solution for this?

chat suggests

USB Selective Suspend - Windows/Linux power management suspends idle USB devices. Can be disabled in OS settings or
via libusb hints.

Device-side timeout - The plate reader itself may go into standby after idle time. The current _recover_transport
only triggers on read timeout, but the connection may appear "alive" while the device is unresponsive.

so _device_initialized = True after hours of idle doesn't mean the device is actually responsive. I am removing the test because it would involve sending a command to the machine as a check, but we are already sending a command to the machine anyway

pylabrobot/plate_reading/tecan/infinite_backend.py

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Lazily initialize the asyncio.Lock to avoid "no current event loop" error on Python 3.9, which requires an event loop when creating locks. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

hazlamshamin · 2026-01-30T16:43:18Z

could you please explain what _MODE_CAPABILITY_COMMANDS are?

are they just more parameters like this?
      f"BEAM DIAMETER={self._capability_numeric('ABS', '#BEAM DIAMETER', 700)}",
that we can add as commands? why not add them?

I'm unable to directly comment to this so I'm quote replying.

_MODE_CAPABILITY_COMMANDS are meant to fetch the capability parameters supported by the machines (in case it is different for other models), as UI does this during initialisation. And yes, they are similar to the line that you quote. The idea was to query those parameters, then save them to be used for downstream commands. However, sometimes, I got errors during querying the full capability commands (the reason why I commented them now and leaving them there as reference). Therefore, I just did the very necessary one now, which is the beam diameter, with safe fallback of the default for the machine.

…cence Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Remove misleading _device_initialized flag that didn't reflect actual device responsiveness - Remove redundant _initialize_device() call from _begin_run() - Call _initialize_device() directly in _recover_transport() after USB recovery Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

hazlamshamin added 2 commits December 20, 2025 18:04

Fix USB capture decode for malformed escape sequences

de9f0a7

Add Tecan Infinite backend and tests

1e61aae

BioCam requested review from BioCam, Copilot and rickwierenga December 20, 2025 17:24

Copilot AI reviewed Dec 20, 2025

View reviewed changes

rickwierenga and others added 6 commits December 20, 2025 12:31

Update pylabrobot/plate_reading/tecan_infinite_backend.py

f50cebe

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update pylabrobot/plate_reading/tecan_infinite_backend.py

db24038

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Guard ASCII frame parsing for incomplete trailers

ca73508

Refine Infinite backend decoders based on DLL plus refactoring

e92c6db

Add Infinite USB lifecycle cleanup and recovery

59ef4e8

Update Infinite backend decoder tests

da96aa2

rickwierenga reviewed Jan 21, 2026

View reviewed changes

pylabrobot/plate_reading/tecan/infinite_backend.py Outdated Show resolved Hide resolved

pylabrobot/plate_reading/tecan/infinite_backend.py Outdated Show resolved Hide resolved

rickwierenga and others added 3 commits January 20, 2026 16:10

remove tecanscanconfig in favor of infinite

9f49e31

rickwierenga mentioned this pull request Jan 21, 2026

Add binary parser #825

Merged

rickwierenga and others added 5 commits January 20, 2026 19:30

Merge branch 'main' into tecan-microplate-reader

0c442a0

Merge branch 'main' into tecan-microplate-reader

6e0119c

Merge branch 'main' into tecan-microplate-reader

14c69fa

Refactor Tecan Infinite backend to use io/binary Reader

bbc0bd9

Replace custom _u16be, _u32be, _i32be helper functions with the Reader class from io/binary using little_endian=False for big-endian parsing. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

move into tecan package

0af381d

rickwierenga mentioned this pull request Jan 21, 2026

Add size parameter to USB read methods #829

Merged

rickwierenga and others added 6 commits January 20, 2026 20:03

Merge main into tecan-microplate-reader

dc783d7

Simplify _end_run to use _active_step_loss_commands directly

0219a2c

Remove redundant step_loss local variable and parameter since _end_run can access self._active_step_loss_commands directly. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Add command verification tests for Tecan Infinite backend

4448f0a

Tests verify that open, close, read_absorbance, read_fluorescence, and read_luminescence send the correct USB commands in the correct order. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Merge branch 'main' into tecan-microplate-reader

d71ff9f

rickwierenga and others added 7 commits January 24, 2026 11:13

Extract common scan loop into _run_scan helper

9bff32c

Reduces duplication across read_absorbance, read_fluorescence, and read_luminescence methods. Also removes unused _active_mode field. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Remove duplicate well computation in _run_scan

1e89fce

Callers now compute ordered_wells and scan_wells once and pass ordered_wells to _run_scan directly. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

remove unused state from configuration

31861e3

Extract common CLEAR commands into _clear_mode_settings helper

98c6490

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Fix type checking errors in decoder _handle_bin methods

4251a5e

Use distinct variable names (cal/data) instead of reusing 'decoded' for both calibration and measurement data decoding to avoid mypy type conflicts. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

rickwierenga reviewed Jan 24, 2026

View reviewed changes

rickwierenga and others added 4 commits January 24, 2026 14:40

Remove packet logging functionality from infinite backend

3dceb24

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

type

073e45e

Fix Python 3.9 compatibility for asyncio.Lock in infinite backend

f407ae2

Lazily initialize the asyncio.Lock to avoid "no current event loop" error on Python 3.9, which requires an event loop when creating locks. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Fix integration time unit conversion

6c970ad

rickwierenga and others added 6 commits January 30, 2026 21:02

Use focal_height parameter for Z position in fluorescence and lumines…

9ea153a

…cence Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Merge branch 'main' into tecan-microplate-reader

0c9ec37

Remove _device_initialized references from tests

9b45fa6

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Add Tecan Infinite 200 PRO to machine overview

156bc63

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Add Tecan Infinite 200 PRO tutorial documentation

a4fb8ef

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Tecan Infinite 200 PRO plate reader backend (Infinite M Plex) #797

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hazlamshamin commented Dec 20, 2025 •

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