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Cannot reproduce the imputation results of SpatialScope #3
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Hi, Thanks for reporting this bug. It seems that we have made some updates to the ConcatCells function. Now, we have updated the tutorial notebook accordingly. Please use git pull to update your local repository. The reason why we set different arrays to run this step is due to the GPU memory limitation, we recommend handle 1000 spots at a time. e.g., 0,1000 means 0 to 1000-th spot Thanks, |
Hi, thanks for your answers. I have a furhter question in the annotation step prior this instruction:
It seems that the pacakges used in the github do not matched its experimental version. Moreover, I am curious about the device requirement for running this model for imputation. I only have one GPU with 40 GB memory, so is it possible for me to run your model for imputation? It seems that I need to call multiple GPU cores for imputation. Thanks. |
Hi, thanks for reporting this bug, we ignored the DeprecationWarning of The minimum GPU requirement for SpatialScope is 2080 Ti (12GB). It's okay to use only one GPU; multiple GPUs were intended to speed up the imputation process. However, limited by GPU memory, we recommend imputing 1000 cells at a time when 40 GB of memory is available. Thanks |
Hi, thanks for your answer. I further meet another problem
It seems that the pydantic provided in the installing process does not match your experiment environment. I wonder if I can access the version of pydantic. Moreover, I wonder if I have cell types for both scRNA-seq and spatial data, can I skip this step (cell-type-identification) for imputation? Thanks. |
Hi, As many reported issues are related to the environment, we have provided a docker image (docker pull xiaojs95/spatialscope) to avoid installation problems. See the project homepage for more details if needed. if cell types for both scRNA-seq and spatial data are available, (cell-type-identification) can be skipped as long as the cell types are matched beween scRNA-seq and spatial data. Thanks, |
Thanks a lot. I will try it and back to you. It seems that you have provided the version of pydantic. Moreover, it seems that the docker file contains the information for installing, same as the environment.yml file provided in your repo, I think it does not make difference if I initially chose to install it based on environment.yml.
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Thanks, after updating pydantic, I addressed my problems of running annotation. However, there seems like another problem of imputing step:
Here is the error. I directly copied the codes from the tutorial. I did have the path shown above. Could you please help me? Thanks. |
Thanks a lot. After fixing this bug, I meet a new error:
I think there exist mismatched information between the cell_class_column and your key for markers. I used the most updated codes. Thanks. |
arguments after --SC_Data were missing |
Thanks a lot, now the training process worked for me. |
Hi, I found a bug in the tutorial for running imputation based on MERFISH dataset:
Moreover, I wonder why we need to set different arrays for running this step:
Thanks a lot.
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