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Minor bug fixes in CLEM workflow when registering grid squares #774

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Merged
tieneupin merged 3 commits into from
Apr 2, 2026
+35 −18
Merged

Minor bug fixes in CLEM workflow when registering grid squares #774

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eb64456
Added rounding when converting caculated pixel values to int
tieneupin Apr 2, 2026
f865be1
Updated comments on GridSquareParameters Pydantic model
tieneupin Apr 2, 2026
5a362d7
Added catch for when image dimensions might get rounded down to 0
tieneupin Apr 2, 2026
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3 changes: 2 additions & 1 deletion src/murfey/util/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -129,10 +129,11 @@ class GridSquareParameters(BaseModel):
tag: str
image: str = ""

# Actual coordinates for image centre in real space
x_location: Optional[float] = None
y_location: Optional[float] = None

# Image coordinates when overlaid on atlas (in pixels0)
# Coordinates for image centre when overlaid on atlas (in pixels)
x_location_scaled: Optional[int] = None
y_location_scaled: Optional[int] = None

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50 changes: 33 additions & 17 deletions src/murfey/workflows/clem/register_preprocessing_results.py
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Expand Up @@ -130,8 +130,12 @@ def _register_clem_imaging_site(
thumbnail_height / result.pixels_y, thumbnail_width / result.pixels_x
)
clem_img_site.thumbnail_pixel_size = result.pixel_size / scaling_factor
clem_img_site.thumbnail_pixels_x = int(result.pixels_x * scaling_factor)
clem_img_site.thumbnail_pixels_y = int(result.pixels_y * scaling_factor)
clem_img_site.thumbnail_pixels_x = (
int(round(result.pixels_x * scaling_factor)) or 1
)
clem_img_site.thumbnail_pixels_y = (
int(round(result.pixels_y * scaling_factor)) or 1
)
murfey_db.add(clem_img_site)
murfey_db.commit()
murfey_db.close()
Expand Down Expand Up @@ -354,30 +358,42 @@ def _register_grid_square(
and clem_img_site.y0 is not None
and clem_img_site.y1 is not None
):
# Find pixel corresponding to image midpoint on atlas
x_mid_real = (
0.5 * (clem_img_site.x0 + clem_img_site.x1) - atlas_entry.x0
)
# Find the real coordinates of the image midpoint
x_mid_real = 0.5 * (clem_img_site.x0 + clem_img_site.x1)
y_mid_real = 0.5 * (clem_img_site.y0 + clem_img_site.y1)

# Find pixel coordinates corresponding to image midpoint on atlas
x_mid_px = int(
x_mid_real / atlas_width_real * atlas_entry.thumbnail_pixels_x
)
y_mid_real = (
0.5 * (clem_img_site.y0 + clem_img_site.y1) - atlas_entry.y0
round(
(x_mid_real - atlas_entry.x0)
/ atlas_width_real
* atlas_entry.thumbnail_pixels_x
)
)
y_mid_px = int(
y_mid_real / atlas_height_real * atlas_entry.thumbnail_pixels_y
round(
(y_mid_real - atlas_entry.y0)
/ atlas_height_real
* atlas_entry.thumbnail_pixels_y
)
)

# Find the size of the image, in pixels, when overlaid on the atlas
width_scaled = int(
(clem_img_site.x1 - clem_img_site.x0)
/ atlas_width_real
* atlas_entry.thumbnail_pixels_x
round(
(clem_img_site.x1 - clem_img_site.x0)
/ atlas_width_real
* atlas_entry.thumbnail_pixels_x
)
or 1
)
height_scaled = int(
(clem_img_site.y1 - clem_img_site.y0)
/ atlas_height_real
* atlas_entry.thumbnail_pixels_y
round(
(clem_img_site.y1 - clem_img_site.y0)
/ atlas_height_real
* atlas_entry.thumbnail_pixels_y
)
or 1
)
else:
logger.warning(
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