From 100256d13c571ef353f2c8e7b9e1568a2d160227 Mon Sep 17 00:00:00 2001
From: Andrey ARISTOV <andrey.aristov@pasteur.fr>
Date: Tue, 30 Apr 2024 15:32:15 +0200
Subject: [PATCH] handle single chip
---
combine.py | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/combine.py b/combine.py
index 10b142e..3f588c8 100644
--- a/combine.py
+++ b/combine.py
@@ -8,12 +8,15 @@ def combine(BF_2D_path:str, TRITC_3D_path:str, out_zarr_path:str):
bd2d = nd2.ND2File(BF_2D_path).to_dask()
print('Opened BF:', bd2d)
fd3d = nd2.ND2File(TRITC_3D_path).to_dask()
+ z_axis = nd2.ND2File(TRITC_3D_path).sizes.index("Z")
print('Opened TRITC:', fd3d)
- fd2d = fd3d.max(axis=1)
- bd2d = da.stack([bd2d, fd2d], axis=1)
+ fd2d = fd3d.max(axis=z_axis)
+ c_axis = fd2d.ndim - 2
+ bd2d = da.stack([bd2d, fd2d], axis=c_axis)
print('Resulting stack:', bd2d)
to_zarr(
- bd2d,
+ bd2d,
+ channel_axis=c_axis,
path=out_zarr_path,
steps=4,
name=['BF','TRITC'],
--
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