diff --git a/src/maldi_tools/extraction.py b/src/maldi_tools/extraction.py index 4af2334..2c84391 100644 --- 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 index d67378d..a61e875 100644 --- 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 TSAI MALDI tiler. 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 TSAI MALDI tiler. 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.**" ] }, {