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STOmics / SAW

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About StereoMap & Image Studio V3.0 #139

Closed sarahshuang closed 1 month ago

sarahshuang commented 1 month ago

Hi,

I am utilizing <StereoMap & Image Studio V3.0> on clouds with C02533C1.cellbin.gef. After changing the counts and its cluster results and save to a new .gef file, I found there is no change to the visulization. I am wondering how this platform can read and show the cluster result of the file.

The code I used: stereo.io.update_gef(data, gef_file='./newC02533C1.cellbin.gef', cluster_res_key='leiden')

Best, Shuang

Clouate commented 1 month ago

@sarahshuang Hi, StereoMap read the information in cellbin.gef['codedCellBlock']. The information is written by SAW, so after running stereo.io.update_gef(), it is necessary to run SAW cellChunk -i cellbin.gef -o output_dir

sarahshuang commented 1 month ago

@sarahshuang Hi, StereoMap read the information in cellbin.gef['codedCellBlock']. The information is written by SAW, so after running stereo.io.update_gef(), it is necessary to run SAW cellChunk -i cellbin.gef -o output_dir

Ah, it seems that there is no cellChunk module for SAW 8.0.1.

Actually, I think I am encountered with a more complex case. First, I had problems in downloading saw v7.0 and other previous versions, so I turned to use your demo data for v8.0, because I only successfully installed saw v8.0.1. However, I found v8.0 cannot get the cellbin result. Then, I thought I need to try Mousekidney(v7.0) again hahahah, so I process the data <.cellbin.gef>, run stereo.io.update_gef() and visulize via your online platform.

Clouate commented 1 month ago

@sarahshuang Hi, for SAW 8.0.1, you could try the following code: /path/to/your/saw-8.0.1/anaconda/bin/python /path/to/your/saw-8.0.1/lib/cellshape/cellShape.pyc -i /path/to/your/cellbin.gef -o output_dir

sarahshuang commented 1 month ago

@sarahshuang Hi, for SAW 8.0.1, you could try the following code: /path/to/your/saw-8.0.1/anaconda/bin/python /path/to/your/saw-8.0.1/lib/cellshape/cellShape.pyc -i /path/to/your/cellbin.gef -o output_dir

Thanks for your kind help! It finally works. =]