TESLA

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GLIBCXX Error when installing

1

Hi, I tried to install Tesla on a ubuntu system a got the following error: **ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version GLIBCXX_3.4.26' not found (required by /home/myusername/.local/share/r-miniconda/envs/SCP_env/lib/python3.8/site-packages/cv2.cpython-38-x86_64-linux-gnu.so)`** Here are the relevant libraries: >...

Jorges1000

No pixel_x key in AnnData object

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Thanks for the great work! The tutorial gives an example on how to convert h5 to h5ad. > #Read original 10x_h5 data and save it to h5ad > from scanpy...

jianggl2000

Dear @jianhuupenn, Hello! Hope you been well. I happen to have a slide that has two tumours and have been struggling to grasp [1] multiple contours [2] individually detect tumor/edge...

jpark27

contour issue

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Hi, I am currently working with biopsy samples in Xenium. In my FFPE slides, I have 3-4 masses for each sample. After using the cv2_detect_contour function, I noticed that only...

jinyeong1316

An error had occurred

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enhanced_exp_adata.obs[g]=enhanced_exp_adata.X[:,enhanced_exp_adata.var.index==g] Traceback (most recent call last): File "/home/ZRZ/miniconda3/envs/TESLA/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2895, in get_loc return self._engine.get_loc(casted_key) File "pandas/_libs/index.pyx", line 70, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 101, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1675,...

rwkw23

Enhanced anndata contains only NaN values for gene expression

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I followed the tutorial using in-house 10X Visium data. I used filtered_feature_bc_matrix.h5, tissue_positions.csv and tissue_hires_image.png as input for Tesla. Countour detection works well using `cnt=tesla.cv2_detect_contour(img, apertureSize=5,L2gradient = True)` . I...

nrosewick

Can TESLA draw the boundaries of regions not based on gene expression, but only provide cluster information?

yliuup

Does TESLA work without providing 'res'?

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Hello, I recently used your tool. Your work is really fancy! I have one question: do you provide an alternative option that can detect the tumor region by the original...

miaz220

Hi, I was following your tutorial and in your original code it seems that cnt will reflect the last step (contour by y, not cv2). I modified to look at...

Jorges1000

Thank you very much for your software. However, when I used tissue_hires_image. png as the input image, The results of enhanced_exp_1data.X are all NA. After consulting the community tutorial, I...

travell1993