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jfnavarro / st_viewer

A GUI tool for easy and smooth visualisation and analysis of Spatial Transcriptomics datasets
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Issue in loading datasets #45

Open mjt-zdz opened 4 years ago

mjt-zdz commented 4 years ago

Hello,

After installing the latest version of ST_Viewer (0.8.5) in Windows, I have been unable to load a dataset on to the platform. I have tried this with several different datasets, but the issue remains the same. The Error message was "Error opening ST Dataset The file does not contain a valid matrix". It should be that the data I use is not standard enough. Maybe you can provide a complete dataset for my reference?The spot coordinates file is missing from the sample data provided.

Thank you!

jfnavarro commented 3 years ago

Hello,

Could you send me the dataset that you are trying to load?

Best, Jose

mjt-zdz commented 3 years ago

Hello,

Thank you for your response! The attachment is the dataset I am trying to load. I download the dataset from https://data.mendeley.com/datasets/29ntw7sh4r/2.

Best, Jinting Ma

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Hello,

Could you send me the dataset that you are trying to load?

Best, Jose

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mjt-zdz commented 3 years ago

Mendeley Data.tar.gz Mendeley Data.zip

jfnavarro commented 3 years ago

Hi Jinting,

The dataset looks correct to me and I was able to load it without a problem.

What steps are you doing to load the dataset? How much RAM memory does your computer has?

Best, Jose

mjt-zdz commented 3 years ago

Hi Jose,

I go to the "Datasets view" and click in the button "Import dataset" and then load the matrix of counts, the HE image and coordinate files on a dialog form to load the dataset. My computer has a RAM memory of 8.00G.

I will try another data loading method.

Best, Jinting

jfnavarro commented 3 years ago

Sorry for missing this out. I believe 8GB is too little RAM. You will have to down-scale your HE image and see if that works. It says in the documentation that is recommended to have minimum 16GB of RAM.