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feat: Add Zarr v2/v3 format support, separate timepoints, and blend bias #17

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feat: Add Zarr v2/v3 format support, separate timepoints, and blend bias #17

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59c7e4a
feat: Add Zarr v2/v3 format support, separate timepoints, and blend bias
Alpaca233 Jan 9, 2026
cb0cd5d
style: Format code with black
Alpaca233 Jan 9, 2026
d22cb97
fix: Add zarr_format field to .zgroup for Zarr v2 scale groups
Alpaca233 Jan 9, 2026
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105 changes: 94 additions & 11 deletions gui/app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -328,6 +328,9 @@ def __init__(
fusion_mode="blended",
flatfield=None,
darkfield=None,
zarr_version=2,
separate_timepoints=False,
blend_bias=0.5,
):
super().__init__()
self.tiff_path = tiff_path
Expand All @@ -337,6 +340,9 @@ def __init__(
self.fusion_mode = fusion_mode
self.flatfield = flatfield
self.darkfield = darkfield
self.zarr_version = zarr_version
self.separate_timepoints = separate_timepoints
self.blend_bias = blend_bias
self.output_path = None

def run(self):
Expand Down Expand Up @@ -379,6 +385,9 @@ def run(self):
downsample_factors=(self.downsample_factor, self.downsample_factor),
flatfield=self.flatfield,
darkfield=self.darkfield,
zarr_version=self.zarr_version,
separate_timepoints=self.separate_timepoints,
blend_bias=self.blend_bias,
)
load_time = time.time() - step_start
self.progress.emit(f"Loaded {tf.n_tiles} tiles ({tf.Y}x{tf.X} each) [{load_time:.1f}s]")
Expand Down Expand Up @@ -702,7 +711,7 @@ class StitcherGUI(QMainWindow):
def __init__(self):
super().__init__()
self.setWindowTitle("Stitcher")
self.setMinimumSize(500, 850)
self.setMinimumSize(500, 950)

self.worker = None
self.output_path = None
Expand Down Expand Up @@ -868,6 +877,31 @@ def setup_ui(self):
settings_layout = QVBoxLayout(settings_group)
settings_layout.setSpacing(8)

# Zarr version selection
zarr_version_layout = QHBoxLayout()
zarr_version_layout.addWidget(QLabel("Output format:"))
self.zarr_version_combo = QComboBox()
self.zarr_version_combo.addItem("Zarr v2 (napari-compatible)", 2)
self.zarr_version_combo.addItem("Zarr v3 (faster, custom viewer)", 3)
self.zarr_version_combo.setCurrentIndex(0) # Default to v2
self.zarr_version_combo.setToolTip(
"Zarr v2: Opens in standard napari and most viewers\n"
"Zarr v3: Better performance with sharding, requires custom viewer button"
)
zarr_version_layout.addWidget(self.zarr_version_combo)
zarr_version_layout.addStretch()
settings_layout.addLayout(zarr_version_layout)

# Separate timepoints option
self.separate_timepoints_checkbox = QCheckBox("Save timepoints as separate files")
self.separate_timepoints_checkbox.setChecked(False)
self.separate_timepoints_checkbox.setToolTip(
"When enabled: Creates t0.ome.zarr, t1.ome.zarr, etc.\n"
"When disabled: All timepoints in single file (default)\n"
"Note: Only applies when dataset has multiple timepoints"
)
settings_layout.addWidget(self.separate_timepoints_checkbox)

self.registration_checkbox = QCheckBox("Enable registration refinement")
self.registration_checkbox.setChecked(False)
self.registration_checkbox.toggled.connect(self.on_registration_toggled)
Expand Down Expand Up @@ -895,14 +929,41 @@ def setup_ui(self):
# Blend pixels (shown when blending enabled)
self.blend_value_widget = QWidget()
self.blend_value_widget.setVisible(False)
blend_value_layout = QHBoxLayout(self.blend_value_widget)
blend_value_layout = QVBoxLayout(self.blend_value_widget)
blend_value_layout.setContentsMargins(20, 0, 0, 0)
blend_value_layout.addWidget(QLabel("Blend pixels:"))
blend_value_layout.setSpacing(8)

# Blend width row
blend_width_row = QHBoxLayout()
blend_width_row.addWidget(QLabel("Blend pixels:"))
self.blend_spin = QSpinBox()
self.blend_spin.setRange(1, 500)
self.blend_spin.setValue(50)
blend_value_layout.addWidget(self.blend_spin)
blend_value_layout.addStretch()
blend_width_row.addWidget(self.blend_spin)
blend_width_row.addStretch()
blend_value_layout.addLayout(blend_width_row)

# Blend bias row
blend_bias_row = QHBoxLayout()
blend_bias_row.addWidget(QLabel("Blend bias:"))
self.blend_bias_slider = QSlider(Qt.Horizontal)
self.blend_bias_slider.setRange(0, 100)
self.blend_bias_slider.setValue(50)
self.blend_bias_slider.setFixedWidth(120)
self.blend_bias_slider.setToolTip(
"Controls left/right tile contribution in overlaps:\n"
"• 50%: Equal blend (default)\n"
"• >50%: Favor left/top tiles\n"
"• <50%: Favor right/bottom tiles"
)
self.blend_bias_slider.valueChanged.connect(self._on_blend_bias_changed)
blend_bias_row.addWidget(self.blend_bias_slider)
self.blend_bias_label = QLabel("50%")
self.blend_bias_label.setFixedWidth(35)
blend_bias_row.addWidget(self.blend_bias_label)
blend_bias_row.addStretch()
blend_value_layout.addLayout(blend_bias_row)

settings_layout.addWidget(self.blend_value_widget)

layout.addWidget(settings_group)
Expand Down Expand Up @@ -1001,6 +1062,9 @@ def on_registration_toggled(self, checked):
def on_blend_toggled(self, checked):
self.blend_value_widget.setVisible(checked)

def _on_blend_bias_changed(self, value):
self.blend_bias_label.setText(f"{value}%")

def on_flatfield_toggled(self, checked):
# Only show/hide flatfield options; preserve any loaded/calculated data
self.flatfield_options_widget.setVisible(checked)
Expand Down Expand Up @@ -1219,15 +1283,21 @@ def run_stitching(self):
if self.blend_checkbox.isChecked():
blend_val = self.blend_spin.value()
blend_pixels = (blend_val, blend_val)
blend_bias = self.blend_bias_slider.value() / 100.0
fusion_mode = "blended"
else:
blend_pixels = (0, 0)
blend_bias = 0.5
fusion_mode = "direct"

# Get flatfield if enabled
flatfield = self.flatfield if self.flatfield_checkbox.isChecked() else None
darkfield = self.darkfield if self.flatfield_checkbox.isChecked() else None

# Get selected zarr version
zarr_version = self.zarr_version_combo.currentData()
separate_timepoints = self.separate_timepoints_checkbox.isChecked()

self.worker = FusionWorker(
self.drop_area.file_path,
self.registration_checkbox.isChecked(),
Expand All @@ -1236,6 +1306,9 @@ def run_stitching(self):
fusion_mode,
flatfield=flatfield,
darkfield=darkfield,
zarr_version=zarr_version,
separate_timepoints=separate_timepoints,
blend_bias=blend_bias,
)
self.worker.progress.connect(self.log)
self.worker.finished.connect(self.on_fusion_finished)
Expand Down Expand Up @@ -1374,12 +1447,22 @@ def open_in_napari(self):
for scale_dir in scale_dirs:
image_path = scale_dir / "image"
if image_path.exists():
store = ts.open(
{
"driver": "zarr3",
"kvstore": {"driver": "file", "path": str(image_path)},
}
).result()
# Try Zarr v3 first, fall back to v2
try:
store = ts.open(
{
"driver": "zarr3",
"kvstore": {"driver": "file", "path": str(image_path)},
}
).result()
except Exception:
# Fall back to Zarr v2
store = ts.open(
{
"driver": "zarr",
"kvstore": {"driver": "file", "path": str(image_path)},
}
).result()
pyramid_data.append(store)

if not pyramid_data:
Expand Down
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