Add workaround for TIFF dimension issue

tools/spot_detection_2d/spot_detection_2d.py

@@ -14,6 +14,7 @@
 import numpy as np
 import pandas as pd
 import scipy.ndimage as ndi
+import tifffile
 from numpy.typing import NDArray
 from skimage.feature import blob_dog, blob_doh, blob_log
 
@@ -36,6 +37,18 @@ def mean_intensity(img: NDArray, y: int, x: int, radius: int) -> float:
         return img[mask].mean()
 
 
+def load_image(fn_in: str) -> NDArray:
+    """
+    Load the input image using ``tifffile`` if possible.
+
+    This is necessary to properly load multi-page TIFF files.
+    """
+    try:
+        return giatools.io.imread(fn_in, impl=tifffile.imread)
+    except tifffile.TiffFileError:
+        return giatools.io.imread(fn_in)  # Not a TIFF file
+
+
 def spot_detection(
     fn_in: str,
     fn_out: str,
@@ -50,7 +63,7 @@ def spot_detection(
 ) -> None:
 
     # Load the single-channel 2-D input image (or stack thereof)
-    stack = giatools.io.imread(fn_in)
+    stack = load_image(fn_in)
 
     # Normalize input image so that it is a stack of images (possibly a stack of a single image)
     assert stack.ndim in (2, 3)
@@ -96,7 +109,7 @@ def spot_detection(
 
     parser = argparse.ArgumentParser(description="Spot detection")
 
-    parser.add_argument("fn_in", help="Name of input image or image sequence (stack).")
+    parser.add_argument("fn_in", help="Name of input image or image stack.")
     parser.add_argument("fn_out", help="Name of output file to write the detections into.")
     parser.add_argument("frame_1st", type=int, help="Index for the starting frame to detect spots (1 for first frame of the stack).")
     parser.add_argument("frame_end", type=int, help="Index for the last frame to detect spots (0 for the last frame of the stack).")

tools/spot_detection_2d/spot_detection_2d.xml

@@ -1,4 +1,4 @@
-<tool id="ip_spot_detection_2d" name="Perform 2-D spot detection" version="0.1" profile="20.05">
+<tool id="ip_spot_detection_2d" name="Perform 2-D spot detection" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description></description>
     <macros>
         <import>creators.xml</import>
@@ -19,6 +19,7 @@
         <requirement type="package" version="1.26.4">numpy</requirement>
         <requirement type="package" version="1.2.4">pandas</requirement>
         <requirement type="package" version="0.21">scikit-image</requirement>
+        <requirement type="package" version="2024.6.18">tifffile</requirement>
     </requirements>
     <command detect_errors="aggressive">
     <![CDATA[
@@ -36,7 +37,7 @@
     ]]>
     </command>
     <inputs>
-        <param name="fn_in" type="data" format="tiff" label="Intensity image or image sequence (stack)" />
+        <param name="fn_in" type="data" format="tiff" label="Intensity image or a stack of images" />
         <param name="frame_1st" type="integer" value="1" label="Starting time point (1 for the first frame of the stack)" />
         <param name="frame_end" type="integer" value="0" label="Ending time point (0 for the last frame of the stack)" />
         <param name="filter_type" type="select" label="Detection filter">
@@ -85,7 +86,7 @@
 
         **Perform spot detection and measure the image intensities.**
 
-        This tool detects spots (blobs) and measures the image intensities in a single-channel 2-D image (or sequence thereof).
+        This tool detects spots (blobs) and measures the image intensities in a single-channel 2-D image (or a stack of such images).
 
         The tool produces a TSV file containing all detections, with the following columns: