The TSAI tiler, unfortunately, does not support .tiff files

angelolab · Nov 28, 2023 · 765fd30 · 765fd30
1 parent 55ee0af
commit 765fd30
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/src/maldi_tools/extraction.py b/src/maldi_tools/extraction.py
@@ -356,7 +356,7 @@ def generate_glycan_mask(
     Args:
     ---
         imz_data (ImzMLParser): The imzML object, needed for coordinate identification.
-        glycan_img_path (Path): Location of the .tiff file containing the glycan scan
+        glycan_img_path (Path): Location of the .png file containing the glycan scan
         glycan_mask_path (Path): Location where the mask will be saved
     """
     validate_paths([glycan_img_path])

diff --git a/templates/maldi-pipeline.ipynb b/templates/maldi-pipeline.ipynb
@@ -583,7 +583,7 @@
     "glycan_img_path = \"path/to/glycan_img.tiff\"\n",
     "\n",
     "# define a save path for your mask\n",
-    "glycan_mask_path = \"path/to/glycan_mask.tiff\"\n",
+    "glycan_mask_path = \"path/to/glycan_mask.png\"\n",
     "\n",
     "# generate and save the glycan mask\n",
     "extraction.generate_glycan_mask(\n",
@@ -597,7 +597,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Each core on the TMA should be appropriately named by the <a href=https://tsai.stanford.edu/research/maldi_tma/>TSAI MALDI tiler</a>. You will need to provide the TIFF saved at `glycan_mask_path` as input. **Ensure that this step is completed before running the following sections.**"
+    "Each core on the TMA should be appropriately named by the <a href=https://tsai.stanford.edu/research/maldi_tma/>TSAI MALDI tiler</a>. You will need to provide the PNG saved at `glycan_mask_path` as input. **Ensure that this step is completed before running the following sections.**"
    ]
   },
   {