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As we can read the data from the sd card.but in compute module 3 plus there is choice between sd card and emmc. if we flash the raspbian os on the emmc and make changes on it then do we read that customized image from the emmc

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I hope I did understand your question correctly. You can also read/copy content of emmc the similar way as you would read sd-card.

I believe you are already using usbboot-tool for flashing image to compute module. Most of the steps stays the same you only need to switch of and if parameters of dd command.

After switch if parameter becomes emmc dev point /dev/rdiskN and of becomes file path for image.

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