SD Card Cloning🔗
If you want to create an SD card image from your PlanktoScope to use on other PlanktoScopes, you can follow the following steps.
Prepare the SD card for cloning🔗
Depending on whether you want to make an SD card image to reuse across multiple machines or whether you only want to make an exact backup of your SD card image, you will need to perform different steps to prepare your SD card for cloning.
Prepare for cloning to reuse in other machines🔗
Normally, your SD card contains some information (a machine-specific ID, system secrets, and SSH secrets) which should never be replicated across multiple PlanktoScopes, and some information (apt package cache) which you would probably consider a waste of space which unnecessarily increases the size of the SD card image you want to make. We provide a preparation script at /usr/libexec/prepare-custom-image to remove this information; it also allows an SD card image created from your SD card to automatically resize itself to match the size of any SD card it's flashed to in the future. After you make any changes you want to make on your PlanktoScope for your SD card image, you should run the preparation script on the PlanktoScope with the command:
Once this script finishes running, it will shut down your PlanktoScope's Raspberry Pi.
Next, you should remove the SD card from your PlanktoScope and plug it into another computer, so that you can clone the SD card into an SD card image; this guide assumes that your other computer runs Linux. With your SD card plugged into your other computer, you can mount the SD card's rootfs partition to delete any other sensitive files which were not removed by the /usr/libexec/prepare-custom-image script. For example, you may also want to delete or edit some or all of the following files from the rootfs partition in order to remove any sensitive or machine-specific information:
/var/lib/overlays/overrides/etc/wpa_supplicant/wpa_supplicant.conf: Wi-Fi configuration and network secrets./home/pi/.ssh/authorized_keys: SSH public keys of devices authorized to remotely connect to the PlanktoScope./home/pi/data/: all images acquired before by the PlanktoScope - this directory may be large, and you probably don't want to copy those datasets across all your other PlanktoScopes./home/pi/.bash_history: Bash command history./home/pi/.python_history: Python command history./home/pi/.gitconfig: Git configuration, which may contain user-specific details.
Info
You can also delete the files listed above before running the /usr/libexec/prepare-custom-image script; the effect is the same. Either way, those files will be permanently deleted on your SD card. However, if you want to keep those files on your SD card, you should make backup copies of those files, and then you can copy those files back onto your SD card after you finish cloning the SD card to an image.
Next, proceed to the Make an SD card image section of this guide.
Prepare an exact backup🔗
If you want to make an exact backup of your SD card and you don't want to reuse your SD card image across multiple PlanktoScopes, then you shouldn't run the /usr/libexec/prepare-custom-image script: that script will delete some files which you probably want to keep. Instead, you should edit the /boot/cmdline.txt file to add the string init=/usr/lib/raspberrypi-sys-mods/firstboot to the end of the file, for example resulting in a file which looks something like:
console=tty1 root=PARTUUID=someuniqueidhere rootfstype=ext4 fsck.repair=yes rootwait init=/usr/lib/raspberrypi-sys-mods/firstboot
Next, you should remove the SD card from your PlanktoScope and plug it into another computer, so that you can clone the SD card into an SD card image; this guide assumes that your other computer runs Linux. Then proceed to the Make an SD card image section of this guide.
Warning
After you have finished cloning the SD card to an SD card image, you should edit the /boot/cmdline.txt file to remove the init=/usr/lib/raspberrypi-sys-mods/firstboot string, before booting up the Raspberry Pi with your SD card again. This will prevent the first-boot script from deleting the SSH server keys already on your SD card.
Make an SD card image🔗
Locate the SD card🔗
Now that your SD card is plugged into a Linux computer, you will need to determine the path of the device file corresponding to your SD card. Usually it will look something like /dev/mmcblk0, /dev/sda, or /dev/sdb; it should always be some file in /dev. To identify the device file for your SD card, run the command sudo fdisk -l in your terminal. The output may look something like:
Disk /dev/nvme0n1: 1.82 TiB, 2000398934016 bytes, 3907029168 sectors
Disk model: WD_BLACK SN770 2TB
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: gpt
Disk identifier: D18C4567-ADF2-4987-987F-CDA411988C8E
Device Start End Sectors Size Type
/dev/nvme0n1p1 2048 1230847 1228800 600M EFI System
/dev/nvme0n1p2 1230848 3327999 2097152 1G Linux filesystem
/dev/nvme0n1p3 3328000 3907028991 3903700992 1.8T Linux filesystem
Disk /dev/mmcblk0: 58.29 GiB, 62587404288 bytes, 122241024 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0xa2033091
To determine which disk device corresponds to your SD card, you should check the size of each device to find the one which approximately matches the size of your SD card. In the above example, the 64 GB SD card is at /dev/mmcblk0.
Next, you should unmount the SD card from your system (or ensure that the device is already not mounted on your system). If you're unsure whether the SD card is mounted, you should use the umount command. For example, if your device is /dev/mmcblk0, you will need to run:
If the devices were already not mounted, you should expect to see (and you can safely ignore) error messages which look like:
Clone the SD card to an image🔗
To clone the Raspberry Pi's SD card to an image file which you can write to other SD cards, you should follow the instructions at https://github.com/mgomesborges/raspberry-pi/blob/master/setup/clone-sd-card.md or https://raspberrytips.com/create-image-sd-card/ . For example, if you are using a Linux computer and the SD card shows up as /dev/mmcblk0, you could run the following command (replacing file paths and names accordingly):
This will create a .img file (at /some/path/here/image-name-here.img) as large as your SD card - make sure you have enough space on your hard drive for the file! If your SD card is large, this process may take a long time; this greatly depends on the speed of your SD card reader. For example, a slow SD card reader may take 30 minutes in order to clone a 32 GB SD card.
Shrink the SD card image🔗
In order to make the SD card practical to share, you should shrink and compress the SD card image file using the PiShrink tool. For example, on Linux you could run the following set of commands (again replacing file paths and names accordingly):
cd /some/path/here
wget https://raw.githubusercontent.com/Drewsif/PiShrink/master/pishrink.sh
chmod +x pishrink.sh
sudo ./pishrink.sh -za image-name-here.img
If you had set up the PlanktoScope software on a Raspberry Pi OS Lite image, you should get a image-name-here.img.gz file which is at least 2 GB in size.
Use the SD card image🔗
You can now use this SD card image with the standard installation guide for installing the PlanktoScope OS on an SD card for one or more PlanktoScopes.