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Add explicit setting for anisotropy rescaling #312

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Merged
ErinWeisbart merged 2 commits into from
Jul 16, 2026
Merged

Add explicit setting for anisotropy rescaling #312

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ab4d54a
Add explicit setting for anisotropy rescaling
bethac07 Jul 15, 2026
f07b02a
typo
ErinWeisbart Jul 16, 2026
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30 changes: 21 additions & 9 deletions active_plugins/runcellpose.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,6 @@
import logging
import sys
import math
import scipy.ndimage

#################################
#
Expand Down Expand Up @@ -120,7 +119,7 @@ class RunCellpose(ImageSegmentation):

module_name = "RunCellpose"

variable_revision_number = 7
variable_revision_number = 8

doi = {
"Please also cite Cellpose when using RunCellpose:": "https://doi.org/10.1038/s41592-020-01018-x",
Expand Down Expand Up @@ -492,6 +491,13 @@ def set_directory_fn(path):
particularly if using a GPU with limited memory. You likely want this off while testing your pipeline.
""")

self.pass_anisotropy = Binary(
text="Rescale for anisotropy?",
value=True,
doc="""\
Allow XYZ resampling to make the volume isotropic. Only used in 3D mode.
""",)

def settings(self):
return [
self.x_name,
Expand Down Expand Up @@ -531,7 +537,8 @@ def settings(self):
self.denoise_type,
self.denoise_image,
self.denoise_name,
self.cache_model
self.cache_model,
self.pass_anisotropy
]

def visible_settings(self):
Expand Down Expand Up @@ -605,6 +612,7 @@ def visible_settings(self):

if self.do_3D.value:
vis_settings.remove(self.stitch_threshold)
vis_settings += [self.pass_anisotropy]

vis_settings += [self.use_averaging, self.use_gpu]

Expand Down Expand Up @@ -676,9 +684,10 @@ def run(self, workspace):
x99 = numpy.percentile(rescale_x, 99)
x_data = numpy.clip((rescale_x - x01) / (x99 - x01), a_min=0, a_max=1)

anisotropy = 0.0
anisotropy = None
if self.do_3D.value:
anisotropy = x.spacing[0] / x.spacing[1]
if self.pass_anisotropy.value:
anisotropy = x.spacing[0] / x.spacing[1]

if self.cellpose_version.value == 'v4':
if self.specify_diameter.value:
Expand Down Expand Up @@ -1211,7 +1220,7 @@ def upgrade_settings(self, setting_values, variable_revision_number, module_name
setting_values = setting_values + ["0.4", "0.0"]
variable_revision_number = 2
if variable_revision_number == 2:
setting_values = setting_values + ["0.0", False, "15", "1.0", False, False]
setting_values = setting_values + ["0.0", 'No', "15", "1.0", 'No', 'No']
variable_revision_number = 3
if variable_revision_number == 3:
setting_values = [setting_values[0]] + ["Python",CELLPOSE_DOCKERS['v2'][0]] + setting_values[1:]
Expand All @@ -1220,15 +1229,18 @@ def upgrade_settings(self, setting_values, variable_revision_number, module_name
setting_values = [setting_values[0]] + ['No'] + setting_values[1:]
variable_revision_number = 5
if variable_revision_number == 5:
setting_values = setting_values + [False]
setting_values = setting_values + ['No']
variable_revision_number = 6
if variable_revision_number == 6:
new_setting_values = setting_values[0:3]
new_setting_values += ['v2', CELLPOSE_DOCKERS['omnipose'][0], setting_values[3], CELLPOSE_DOCKERS['v3'][0], CELLPOSE_DOCKERS['v4'][0]]
new_setting_values += [False, setting_values[4], MODEL_NAMES['omnipose'][0], setting_values[5], MODEL_NAMES['v3'][0], MODEL_NAMES['v4'][0]]
new_setting_values += setting_values[6:]+ [False, DENOISER_NAMES[0], False, "Preprocessed", False]
new_setting_values += ['No', setting_values[4], MODEL_NAMES['omnipose'][0], setting_values[5], MODEL_NAMES['v3'][0], MODEL_NAMES['v4'][0]]
new_setting_values += setting_values[6:]+ ['No', DENOISER_NAMES[0], 'No', "Preprocessed", 'No']
setting_values = new_setting_values
variable_revision_number = 7
if variable_revision_number ==7:
setting_values = setting_values + ['Yes']
variable_revision_number = 8
return setting_values, variable_revision_number


Expand Down