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Did SAW 7.1 use stereopy to perform cell segmentation? #112

Open yemao701 opened 1 month ago

yemao701 commented 1 month ago

I wonder if I performed cell segmentation using SAW7.1, should I refine cell segmentation using stereopy. Thank you very much for your time !

Clouate commented 1 month ago

Hi, SAW 7.1 automatically uses Stereopy to perform cell segmentation if you set the parameter '-doCellBin' as 'Y' when run the _Scripts/stereoPipelinev7.1.sh, and the method is Deep Learning Model V3

yemao701 commented 1 month ago

Hi, SAW 7.1 automatically uses Stereopy to perform cell segmentation if you set the parameter '-doCellBin' as 'Y' when run the _Scripts/stereoPipelinev7.1.sh, and the method is Deep Learning Model V3

While processing four stereo-seq Chips, I found that three of them couldn't be register automatically and needed manual registration. After manually register the three chips, two of them proceeded normally in the subsequent process, but one chip showed an error after successfully running the manual alignment (manualRegister) and then running ipr2img: 'The tar package name is inconsistent with the QCResultFile name'. I re-ran the image QC using ImageStudio from scratch, but still got the same error. Have you encountered a similar situation before？ image

Clouate commented 1 month ago

While processing four stereo-seq Chips, I found that three of them couldn't be register automatically and needed manual registration. After manually register the three chips, two of them proceeded normally in the subsequent process, but one chip showed an error after successfully running the manual alignment (manualRegister) and then running ipr2img: 'The tar package name is inconsistent with the QCResultFile name'. I re-ran the image QC using ImageStudio from scratch, but still got the same error. Have you encountered a similar situation before？ image

Hi, the .ipr file and the .tar.gz file shoule be consistent. Maybe you have changed the name of the .tar.gz file? It is recommended that you could use the original .tar.gz file for the input, or you could try to use the python package h5py to get the corresponding .tar.gz file name in the ipr file, and use it to rename your tar.gz.

For example, if the stain type of your image is ssDNA,

import h5py
h5py.File('C03537F1_SC_20240528_175523_3.0.4.ipr')['ssDNA']['ImageInfo'].attrs['QCResultFile']

Then, if the output is 'C03537F1_SC_20240528_175523_3.0.4', change the name of .tar.gz to C03537F1_SC_20240528_175523_3.0.4.tar.gz