Error in "Loading the data and QC" Step

[jade-minzlaff]

Hello, thank you for creating a tool for deconvolution of Visium HD data! I was very excited to find your publication and this GitHub page. I have a VisiumHD dataset and I have a table of known cell type markers for my tissue type from a public single cell RNA seq dataset. My goal is to use these known cell type markers to assign cell type labels to all 8 um bins in my dataset, which your tool, Easydecon, looks perfect for.

My issue is that when I get to the "Loading the data and QC step", I keep getting an error about my "tissue_highres_image" file, even though it exists in the expected location, it keeps throwing an error. The only difference I can see is that my full resolution image file is a .tif file instead of the .btf file used in the example notebooks, but that doesn't seem to be the source of the error. I am using the easydecon conda environment. Please let me know if you have suggestions for me to me successfully upload my data and use EasyDecon!

A screenshot is attached, this is the code I am running:

bin_size=8
sample_id="FN706"

sdata=spatialdata_io.visium_hd("C:/Users/user/Desktop/Visium HD data/Batch1_Reanalysis_112524/analysis/spaceranger/FN706/H1-PZ6GV8J_D1_FN706_mGEXv2HD/outs/binned_outputs/",fullres_image_file="C:/Users/user/Desktop/Visium HD data/Batch1_Reanalysis_112524/analysis/spaceranger/FN706/FN706 Recut.tif",
bin_size=bin_size,dataset_id=sample_id,load_all_images=True)
sdata

and I recieve the error:

---

KeyError Traceback (most recent call last)
Cell In[5], line 4
1 bin_size=8
2 sample_id="FN706"
----> 4 sdata=spatialdata_io.visium_hd("C:/Users/user/Desktop/Visium HD data/Batch1_Reanalysis_112524/analysis/spaceranger/FN706/H1-PZ6GV8J_D1_FN706_mGEXv2HD/outs/binned_outputs/",fullres_image_file="C:/Users/user/Desktop/Visium HD data/Batch1_Reanalysis_112524/analysis/spaceranger/FN706/FN706 Recut.tif",
5 bin_size=bin_size,dataset_id=sample_id,load_all_images=True)
6 sdata

File c:\Users\user\miniconda3\envs\easydecon\lib\site-packages\spatialdata_io\readers\visium_hd.py:292, in visium_hd(path, dataset_id, filtered_counts_file, bin_size, bins_as_squares, fullres_image_file, load_all_images, imread_kwargs, image_models_kwargs, anndata_kwargs)
286 # hires image
287 load_image(
288 path=path / VisiumHDKeys.IMAGE_HIRES_FILE,
289 suffix="_hires_image",
290 )
291 set_transformation(
--> 292 images[dataset_id + "_hires_image"],
293 {"downscaled_hires": Identity()},
294 set_all=True,
295 )
297 # lowres image
298 load_image(
299 path=path / VisiumHDKeys.IMAGE_LOWRES_FILE,
300 suffix="_lowres_image",
301 )

KeyError: 'FN706_hires_image'

[sinanugur]

Hi @jade-minzlaff ,

Thanks for your interest in Easydecon. This might be the version of the SpatialData package. I think different versions have different input file constraints. If you install Easydecon in a clean environment, it should not be a problem. Also I did not test the package for Windows but as long as the correct versions installed, it should not be an issue.

Can you send the version of the loaded packages?

You can run this after you loaded the packages so I can see the versions:

import sys

for module_name, module in sys.modules.items():
    if module_name and hasattr(module, '__version__'):
        print(f"{module_name}: {module.__version__}")