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Rename and update example script, add slides #42

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Dec 4, 2023
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Rename and update example script, add slides #42

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7ac8aef
Rename and update example script
imagejan Nov 30, 2023
dcd699e
Remove unnecessary print statement
imagejan Nov 30, 2023
1114879
Add slides illustrating various config arguments
imagejan Dec 4, 2023
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Binary file added presentations/faim-wako-searchfirst_overview.pdf
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3 changes: 3 additions & 0 deletions presentations/faim-wako-searchfirst_overview.pdf.license
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
SPDX-FileCopyrightText: 2023 Friedrich Miescher Institute for Biomedical Research (FMI), Basel (Switzerland)

SPDX-License-Identifier: MIT
4 changes: 2 additions & 2 deletions scripts/simple_segmentation.py → scripts/searchfirst.py
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Expand Up @@ -3,8 +3,8 @@
# SPDX-License-Identifier: MIT

"""SearchFirst script to run a simple segmentation."""
import typer as typer
from faim_wako_searchfirst.segment import run
import typer
from faim_wako_searchfirst.main import run


def main(folder_path: str):
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1 change: 0 additions & 1 deletion src/faim_wako_searchfirst/sample.py
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Expand Up @@ -26,7 +26,6 @@ def dense_grid(
block_size=(binning_factor, binning_factor),
func=np.max,
)
print(downscaled.shape)
with open(output_path, "w", newline="") as csv_file:
c = csv.writer(csv_file)
count = 0
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