yifan wang

[Bug]ArrowInvalid: Parquet magic bytes not found in footer. Either the file is corrupted or this is not a parquet file.

2

## Description I try to learn the sopa with example data. Here is the code I copy from example file. patches = sopa.segmentation.Patches2D(sdata, image_key, patch_width=1200, patch_overlap=50) patches.write() from sopa._sdata import...

[Bug]Invalid element type: <class 'xarray.core.dataarray.DataArray'>

3

## Description Same example dataset. Rerun the code and get new error. ## Reproducing the issue ValueError: Invalid element type: ## Expected behavior A clear and concise description of what...

3D visualize

1

Hi developer. Thanks alot for the useful tools and sorry for keep bothering. I need a 3D visualiza on my xenium dataset. Now I can correctly load my xenium data...

How to transfer xenium dataset to Anndata which could be used for 3D visualization

6

Hi developer. I'm wondering how to transfer the xenium dataset to anndata which could be used for 3D visualization. And also for the example, where we can downalod the "E7-9h_cellbin_h5ad.zip"

pip下载安装的时候显示错误

6

Hi, I I tried with pip install and got this error. cl : Command line error D8021 : invalid numeric argument '/Wno-unused-variable' Thank you

Hi Thanks for the package. I encountered a weird problem. I started from the very beginning by running conda env create -f environment.yml, but I got an error that says...

[Bug]"Could not find element with name ['cell_circles']"

7

Dear Developer, I'm trying to use the sopa to output the xenium file, so I can open it with xenium. but I got the error said no cell circles, I...

Alignment image with xenium

24

Sorry for the continuous questions, and I'm really at the beginning stage of spatial transcriptomics. I aligned my confocal image (Z-stack OME TIFF file) with the Xenium dataset in Xenium...

Hi developer, I'm trying to train my own data. I checked the tutorial but it is not clear. I followed the tutorial and set the config_train.yml training: dataset_dir: /projectnb/mylabscc/yzw0093/Train_dataset/Plantseg/data/train/images #...