adding anisotropy param to make_train.py

MouseLand · Sep 12, 2024 · d35083d · d35083d
1 parent f10df0d
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Showing 2 changed files with 15 additions and 5 deletions.
diff --git a/cellpose/gui/make_train.py b/cellpose/gui/make_train.py
@@ -37,6 +37,9 @@ def main():
     input_img_args.add_argument(
         '--all_channels', action='store_true', help=
         'use all channels in image if using own model and images with special channels')
+    input_img_args.add_argument("--anisotropy", required=False, default=1.0, type=float,
+                                help="anisotropy of volume in 3D")
+
 
     # algorithm settings
     algorithm_args = parser.add_argument_group("algorithm arguments")
@@ -74,6 +77,8 @@ def main():
             print(npm[p], img[0].shape)
             Ly, Lx = img.shape[1:3]
             imgs = img[np.random.permutation(img.shape[0])[:args.nimg_per_tif]]
+            if args.anisotropy > 1.0:
+                imgs = transforms.resize_image(imgs, Ly=int(args.anisotropy * Ly), Lx=Lx)
             for k, img in enumerate(imgs):
                 if args.tile_norm:
                     img = transforms.normalize99_tile(img, blocksize=args.tile_norm)

diff --git a/docs/train.rst b/docs/train.rst
@@ -133,15 +133,18 @@ the overall normalization scaling on the full images, e.g. ``normalize={"percent
 a notebook for example with ``from cellpose import transforms; plt.imshow(transforms.normalize99(img, lower=3, upper=98))``. The default 
 that will be used for training on the image crops is ``[1, 99]``. 
 
-You can create image crops from z-stacks (in XY, YZ and XZ) using the script ``cellpose/gui/make_train.py``:
+You can create image crops from z-stacks (in YX, YZ and XZ) using the script ``cellpose/gui/make_train.py``. 
+If you have anisotropic volumes, then set the ``--anisotropy`` flag to the ratio between pixel size in Z and in YX, 
+e.g. set ``--anisotropy 5`` for pixel size of 1.0 um in YX and 5.0 um in Z. 
+See the help message for more information:
 
 ::
     
-    python cellpose/gui/make_train.py --help
+    python cellpose\gui\make_train.py --help
     usage: make_train.py [-h] [--dir DIR] [--image_path IMAGE_PATH] [--look_one_level_down] [--img_filter IMG_FILTER]
                         [--channel_axis CHANNEL_AXIS] [--z_axis Z_AXIS] [--chan CHAN] [--chan2 CHAN2] [--invert]
-                        [--all_channels] [--sharpen_radius SHARPEN_RADIUS] [--tile_norm TILE_NORM]
-                        [--nimg_per_tif NIMG_PER_TIF] [--crop_size CROP_SIZE]
+                        [--all_channels] [--anisotropy ANISOTROPY] [--sharpen_radius SHARPEN_RADIUS]
+                        [--tile_norm TILE_NORM] [--nimg_per_tif NIMG_PER_TIF] [--crop_size CROP_SIZE]
 
     cellpose parameters
 
@@ -164,6 +167,8 @@ You can create image crops from z-stacks (in XY, YZ and XZ) using the script ``c
     --chan2 CHAN2         nuclear channel (if cyto, optional); 0: NONE, 1: RED, 2: GREEN, 3: BLUE. Default: 0
     --invert              invert grayscale channel
     --all_channels        use all channels in image if using own model and images with special channels
+    --anisotropy ANISOTROPY
+                            anisotropy of volume in 3D
 
     algorithm arguments:
     --sharpen_radius SHARPEN_RADIUS
@@ -173,4 +178,4 @@ You can create image crops from z-stacks (in XY, YZ and XZ) using the script ``c
     --nimg_per_tif NIMG_PER_TIF
                             number of crops in XY to save per tiff. Default: 10
     --crop_size CROP_SIZE
-                            size of random crop to save. Default: 512
+                            size of random crop to save. Default: 512