diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py index a5b54fe966a0f18477e4af7b18772ea1123e512b..08f87b68666b1a9838a2f1f2c5dfd45021d05d05 100644 --- a/2d_spots_in_fibers.py +++ b/2d_spots_in_fibers.py @@ -2,7 +2,7 @@ #@ CommandService command #@ File (label="select image", description="select your input image", style=file) path_to_image #@ Integer (label="select image file series", description="leave 1 if not needed", value=1, min=1, max=20, stepSize=1, persist=false, style=slider) series_number -#@ Integer (label="Fiber Segmentation", description="select the Fiber Segmentation RoiSet .zip file") fiber_segmentation_roiset +#@ File (label="Fiber Segmentation", description="select the Fiber Segmentation RoiSet .zip file", style=file) fiber_segmentation_roiset #@ Integer (label="DAPI channel", description="select the DAPI channel", min=1, max=20, stepSize=1, persist=true, style=slider) dapi_channel_number #@ Integer (label="DAPI threshold", description="0 = Auto", min=0) threshold #@ String (label="processing channels", description="comma separated list of channels, e.g. 2,3,6,7", value="1,2,3,4") processing_channels_string @@ -748,6 +748,7 @@ def close_images(list_of_imps): path_to_image = str(path_to_image).replace("\\","/") +fiber_segmentation_roiset = str(fiber_segmentation_roiset).replace("\\","/") parent_dir, filename, ext = get_parentdir_filename_ext_from_path(path_to_image) write_bf_memoryfile(path_to_image) n_channels, image_width, image_height, bit_depth = get_ome_metadata(path_to_image, series_number)