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quick calibration for 4x and 20x objectives on cytation1 w/ 1288x964 pixel Blackfly BFLY-U3-13S2M sensor #590

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quick calibration for 4x and 20x objectives on cytation1 w/ 1288x964 pixel Blackfly BFLY-U3-13S2M sensor #590

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quick calibration 4x 20x
ben-ray Jun 29, 2025
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switch to strings to fix autoreload issues
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switch to strings to fix issues with autoreload
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2 changes: 1 addition & 1 deletion pylabrobot/plate_reading/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
from .biotek_backend import Cytation5Backend, Cytation5ImagingConfig
from .biotek_backend import Cytation5Backend, CytationImagingConfig
from .clario_star_backend import CLARIOStarBackend
from .image_reader import ImageReader
from .imager import Imager
Expand Down
39 changes: 28 additions & 11 deletions pylabrobot/plate_reading/biotek_backend.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,8 +77,12 @@ async def _golden_ratio_search(
return (b + a) / 2


CytationModel = Literal["cytation1", "cytation5"]


@dataclass
class Cytation5ImagingConfig:
class CytationImagingConfig:
model: CytationModel = "cytation5"
camera_serial_number: Optional[str] = None
max_image_read_attempts: int = 8

Expand All @@ -87,6 +91,19 @@ class Cytation5ImagingConfig:
filters: Optional[List[Optional[ImagingMode]]] = None


_FOV: dict[str, dict[float, tuple[float, float]]] = {
"cytation1": {
4: (1288 / 596, 964 / 596),
20: (1288 / 3000, 964 / 3000),
Comment on lines +96 to +97
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what is going on with these denominators?

for the cytation5, it's to convert um to mm

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@ben-ray ben-ray Jun 30, 2025 •
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The cytation5 sensor is 2448x2048 while the cytation1 is 1288x964. The scaling factor from pixel to micron will be identical for both axis, but why does the image_size conversion not take the sensor size into account? I would expect the X and Y size to be different but the scaling factor is identical in X and Y in the original Cytation5 implementation.

These numbers are my attempt to account for the significantly different x and y size of my sensor (my pixels are still perfectly square)

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this is not a scaling factor

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@ben-ray ben-ray Jun 30, 2025 •
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Then how do I determine these and why are they not different for X and Y on the cytation5?

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i took the number from gen5.exe, and then did um -> mm conversion which seems to work

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at least it corresponds with their firmware commands.

you can use a firmware command to check

},
"cytation5": {
4: (3474 / 1000, 3474 / 1000),
20: (694 / 1000, 694 / 1000),
40: (347 / 1000, 347 / 1000),
},
}


class Cytation5Backend(ImageReaderBackend):
"""Backend for biotek cytation 5 image reader.

Expand All @@ -98,16 +115,15 @@ def __init__(
self,
timeout: float = 20,
device_id: Optional[str] = None,
imaging_config: Optional[Cytation5ImagingConfig] = None,
imaging_config: Optional[CytationImagingConfig] = None,
) -> None:
super().__init__()
self.timeout = timeout

self.io = FTDI(device_id=device_id)

self.spinnaker_system: Optional["PySpin.SystemPtr"] = None
self.cam: Optional["PySpin.CameraPtr"] = None
self.imaging_config = imaging_config or Cytation5ImagingConfig()
self.imaging_config = imaging_config or CytationImagingConfig()
self._filters: Optional[List[Optional[ImagingMode]]] = self.imaging_config.filters
self._objectives: Optional[List[Optional[Objective]]] = self.imaging_config.objectives
self._version: Optional[str] = None
Expand Down Expand Up @@ -1173,16 +1189,17 @@ def image_size(magnification: float) -> Tuple[float, float]:
# "wide fov" is an option in gen5.exe, but in reality it takes the same pictures. So we just
# simply take the wide fov option.
# um to mm (plr unit)
if magnification == 4:
return (3474 / 1000, 3474 / 1000)
if magnification == 20:
return (694 / 1000, 694 / 1000)
if magnification == 40:
return (347 / 1000, 347 / 1000)
raise ValueError(f"Don't know image size for magnification {magnification}")
try:
size = _FOV[self.imaging_config.model][magnification]
except KeyError:
raise ValueError(
f"Don't know image size for model {self.imaging_config.model} and magnification {magnification}"
)
return size

if self._objective is None:
raise RuntimeError("Objective not set. Run set_objective() first.")

magnification = self._objective.magnification
img_width, img_height = image_size(magnification)

Expand Down