diff --git a/.github/workflows/build-os.yml b/.github/workflows/build-os.yml
index 3ffaa6a1c..32bb3678a 100644
--- a/.github/workflows/build-os.yml
+++ b/.github/workflows/build-os.yml
@@ -200,7 +200,7 @@ jobs:
           user: pi
           run: |
             export DEBIAN_FRONTEND=noninteractive
-            cd /home/pi/PlanktoScope
+            cd /opt/PlanktoScope
             just ci
 
       # UPLOAD OS IMAGE
diff --git a/backend/planktoscope-org.backend.service b/backend/planktoscope-org.backend.service
index 448bf1af3..eac9cac08 100644
--- a/backend/planktoscope-org.backend.service
+++ b/backend/planktoscope-org.backend.service
@@ -5,7 +5,7 @@ After=mosquitto.service
 
 [Service]
 Type=simple
-ExecStart=/home/pi/PlanktoScope/backend/src/service.js
+ExecStart=/opt/PlanktoScope/backend/src/service.js
 Restart=on-failure
 
 User=pi
diff --git a/controller/bubbler/planktoscope-org.controller.bubbler.service b/controller/bubbler/planktoscope-org.controller.bubbler.service
index 5976a09a0..0ee3655d8 100644
--- a/controller/bubbler/planktoscope-org.controller.bubbler.service
+++ b/controller/bubbler/planktoscope-org.controller.bubbler.service
@@ -5,7 +5,7 @@ After=mosquitto.service
 [Service]
 Type=simple
 Environment=HOME=/home/pi
-WorkingDirectory=/home/pi/PlanktoScope/controller
+WorkingDirectory=/opt/PlanktoScope/controller
 ExecStart=/usr/local/bin/uv run python -m bubbler.main
 User=pi
 Group=pi
diff --git a/controller/display/planktoscope-org.controller.display.service b/controller/display/planktoscope-org.controller.display.service
index ec33a6af4..2dbc52e8b 100644
--- a/controller/display/planktoscope-org.controller.display.service
+++ b/controller/display/planktoscope-org.controller.display.service
@@ -5,7 +5,7 @@ After=mosquitto.service
 [Service]
 Type=simple
 Environment=HOME=/home/pi
-WorkingDirectory=/home/pi/PlanktoScope/controller
+WorkingDirectory=/opt/PlanktoScope/controller
 ExecStart=/usr/local/bin/uv run python -m display.main
 User=pi
 Group=pi
diff --git a/controller/focus/main.py b/controller/focus/main.py
index 30a50f7e0..104f8acf3 100644
--- a/controller/focus/main.py
+++ b/controller/focus/main.py
@@ -34,7 +34,7 @@ async def start() -> None:
 
     hardware_config = None
     try:
-        async with aiofiles.open("/home/pi/PlanktoScope/hardware.json", mode="r") as file:
+        async with aiofiles.open("/opt/PlanktoScope/hardware.json", mode="r") as file:
             hardware_config = json.loads(await file.read())
     except FileNotFoundError:
         return None
diff --git a/controller/focus/planktoscope-org.controller.focus.service b/controller/focus/planktoscope-org.controller.focus.service
index 9ed72f79b..c0b589579 100644
--- a/controller/focus/planktoscope-org.controller.focus.service
+++ b/controller/focus/planktoscope-org.controller.focus.service
@@ -5,7 +5,7 @@ After=mosquitto.service
 [Service]
 Type=simple
 Environment=HOME=/home/pi
-WorkingDirectory=/home/pi/PlanktoScope/controller
+WorkingDirectory=/opt/PlanktoScope/controller
 ExecStart=/usr/local/bin/uv run python -m focus.main
 User=pi
 Group=pi
diff --git a/controller/helpers.py b/controller/helpers.py
index d4b8bf50a..a1618b85d 100644
--- a/controller/helpers.py
+++ b/controller/helpers.py
@@ -7,7 +7,7 @@
 import aiomqtt
 import paho
 
-HARDWARE_CONFIG_PATH = "/home/pi/PlanktoScope/hardware.json"
+HARDWARE_CONFIG_PATH = "/opt/PlanktoScope/hardware.json"
 hardwre_config_lock = asyncio.Lock()
 
 
diff --git a/controller/imager/main.py b/controller/imager/main.py
index 163c714bf..b7da6e504 100644
--- a/controller/imager/main.py
+++ b/controller/imager/main.py
@@ -529,7 +529,7 @@ def close(self) -> None:
 def read_config() -> typing.Any:
     config = {}
     try:
-        with open("/home/pi/PlanktoScope/hardware.json", "r") as file:
+        with open("/opt/PlanktoScope/hardware.json", "r") as file:
             try:
                 config = json.load(file)
             except Exception:
diff --git a/controller/imager/planktoscope-org.controller.imager.service b/controller/imager/planktoscope-org.controller.imager.service
index b7a109d36..3a2448d5c 100644
--- a/controller/imager/planktoscope-org.controller.imager.service
+++ b/controller/imager/planktoscope-org.controller.imager.service
@@ -7,7 +7,7 @@ After=mediamtx.service
 [Service]
 Type=simple
 Environment=HOME=/home/pi
-WorkingDirectory=/home/pi/PlanktoScope/controller
+WorkingDirectory=/opt/PlanktoScope/controller
 # FIXME: https://github.com/fairscope/PlanktoScope/issues/842
 ExecStartPre=/bin/sleep 5
 ExecStart=/usr/local/bin/uv run python -m imager.main
diff --git a/controller/light/LM36011.py b/controller/light/LM36011.py
index 3216e0eba..1eb1d6214 100644
--- a/controller/light/LM36011.py
+++ b/controller/light/LM36011.py
@@ -24,7 +24,7 @@ class Register(enum.IntEnum):
     DEFAULT_CURRENT = 10
 
     def __init__(self):
-        with open("/home/pi/PlanktoScope/hardware.json", "r") as file:
+        with open("/opt/PlanktoScope/hardware.json", "r") as file:
             config = json.load(file)
             hat_version = float(config.get("hat_version") or 0)
             # The led is controlled by LM36011
diff --git a/controller/light/planktoscope-org.controller.light.service b/controller/light/planktoscope-org.controller.light.service
index 3279f00f4..1ff79794b 100644
--- a/controller/light/planktoscope-org.controller.light.service
+++ b/controller/light/planktoscope-org.controller.light.service
@@ -5,7 +5,7 @@ After=mosquitto.service
 [Service]
 Type=simple
 Environment=HOME=/home/pi
-WorkingDirectory=/home/pi/PlanktoScope/controller
+WorkingDirectory=/opt/PlanktoScope/controller
 ExecStart=/usr/local/bin/uv run python -m light.main
 User=pi
 Group=pi
diff --git a/controller/planktoscope-org.controller.service b/controller/planktoscope-org.controller.service
index 91ea393b2..a53c5aa78 100644
--- a/controller/planktoscope-org.controller.service
+++ b/controller/planktoscope-org.controller.service
@@ -8,7 +8,7 @@ After=mediamtx.service
 [Service]
 Type=simple
 Environment=HOME=/home/pi
-WorkingDirectory=/home/pi/PlanktoScope/controller
+WorkingDirectory=/opt/PlanktoScope/controller
 ExecStart=/usr/local/bin/uv run main.py
 User=pi
 Group=pi
diff --git a/controller/pump/planktoscope-org.controller.pump.service b/controller/pump/planktoscope-org.controller.pump.service
index 794dea573..69d02f5bb 100644
--- a/controller/pump/planktoscope-org.controller.pump.service
+++ b/controller/pump/planktoscope-org.controller.pump.service
@@ -5,7 +5,7 @@ After=mosquitto.service
 [Service]
 Type=simple
 Environment=HOME=/home/pi
-WorkingDirectory=/home/pi/PlanktoScope/controller
+WorkingDirectory=/opt/PlanktoScope/controller
 ExecStart=/usr/local/bin/uv run python -m pump.main
 User=pi
 Group=pi
diff --git a/documentation/docs/community/contribute/tips-and-tricks.md b/documentation/docs/community/contribute/tips-and-tricks.md
index 50e7f66f3..3ac5ebb42 100644
--- a/documentation/docs/community/contribute/tips-and-tricks.md
+++ b/documentation/docs/community/contribute/tips-and-tricks.md
@@ -39,7 +39,7 @@ PlanktoScope OS is ready.
 Type the following commands
 
 ```sh
-cd /home/pi/PlanktoScope
+cd /opt/PlanktoScope
 just update
 # don't forget to copy default configs if needed/wanted
 # cp default-configs/v3.0.hardware.json hardware.json
@@ -99,7 +99,7 @@ You can now SSH into your PlanktoScope without username / password (using `ssh $
     <summary>On the PlanktoScope</summary>
 
 ```sh
-cd ~/PlanktoScope
+cd /opt/PlanktoScope
 just developer-mode
 git checkout main
 git status
@@ -107,7 +107,7 @@ git status
 
 </details>
 
-We recommend developping directly from the PlanktoScope using [Visual Studio Code and the Remote - SSH extension](https://code.visualstudio.com/docs/remote/ssh) or [Zed - Remote Development](https://zed.dev/docs/remote-development). Use `$planktoscope` as the host to connect to and open the `/home/pi/PlanktoScope` directory.
+We recommend developping directly from the PlanktoScope using [Visual Studio Code and the Remote - SSH extension](https://code.visualstudio.com/docs/remote/ssh) or [Zed - Remote Development](https://zed.dev/docs/remote-development). Use `$planktoscope` as the host to connect to and open the `/opt/PlanktoScope` directory.
 
 ## Connect to router
 
diff --git a/documentation/docs/operation/software-upgrades.md b/documentation/docs/operation/software-upgrades.md
index 60fb12d9f..9abe5cd87 100644
--- a/documentation/docs/operation/software-upgrades.md
+++ b/documentation/docs/operation/software-upgrades.md
@@ -16,7 +16,7 @@ Before you reset/upgrade/downgrade the software installed on your PlanktoScope,
 
 Advanced users may also want to take the following actions, depending on what changes they have made:
 
-- If you don't want to write down your white balance gains and hardware settings/calibrations, you can instead back up your PlanktoScope's hardware settings file, which is saved at `/home/pi/PlanktoScope/hardware.json`, for example in the file browser at <http://planktoscope.local/admin/fs/files/home/pi/PlanktoScope/> . This file includes some hidden settings not exposed in the PlanktoScope's Node-RED dashboard - so if you have changed any such settings by editing this file, then you may want to back up this file.
+- If you don't want to write down your white balance gains and hardware settings/calibrations, you can instead back up your PlanktoScope's hardware settings file, which is saved at `/opt/PlanktoScope/hardware.json`, for example in the file browser at <http://planktoscope.local/admin/fs/files/opt/PlanktoScope/> . This file includes some hidden settings not exposed in the PlanktoScope's Node-RED dashboard - so if you have changed any such settings by editing this file, then you may want to back up this file.
 
 ## Reset the PlanktoScope OS
 
diff --git a/justfile b/justfile
index 899a25ce3..0200a7f40 100644
--- a/justfile
+++ b/justfile
@@ -75,6 +75,7 @@ developer-mode: setup-dev
 reset: base setup
     rm /home/pi/PlanktoScope/config.json
     rm /home/pi/PlanktoScope/hardware.json
+    rm /home/pi/PlanktoScope/calibration.json
     sudo reboot
 
 install-uv:
diff --git a/lib/cockpit.js b/lib/cockpit.js
index 32dff399b..2ee4e4bac 100644
--- a/lib/cockpit.js
+++ b/lib/cockpit.js
@@ -6,7 +6,7 @@ import { Systemctl } from "systemctl.js"
 import { randomUUID } from "node:crypto"
 import { queue } from "./helpers.js"
 
-const config_template_path = "/home/pi/PlanktoScope/os/cockpit/cockpit.ini"
+const config_template_path = "/opt/PlanktoScope/os/cockpit/cockpit.ini"
 const config_path = "/etc/cockpit/cockpit.conf"
 
 async function configureCockpit({ hostname, address } = {}) {
diff --git a/lib/file-config.js b/lib/file-config.js
index a62c10f28..57d2abd67 100644
--- a/lib/file-config.js
+++ b/lib/file-config.js
@@ -1,10 +1,11 @@
-import { rm, writeFile } from "fs/promises"
+import { rm, writeFile, mkdir } from "fs/promises"
 import { readFile, access, constants, copyFile } from "fs/promises"
 
 const HARDWARE_PATH = "/home/pi/PlanktoScope/hardware.json"
 const SOFTWARE_PATH = "/home/pi/PlanktoScope/config.json"
 const CALIBRATION_PATH = "/home/pi/PlanktoScope/calibration.json"
-const CALIBRATION_DEFAULTS_PATH = "/home/pi/PlanktoScope/default-configs/calibration.json"
+const CALIBRATION_DEFAULTS_PATH =
+  "/opt/PlanktoScope/default-configs/calibration.json"
 
 async function hasConfig(path) {
   try {
@@ -16,14 +17,16 @@ async function hasConfig(path) {
 }
 
 export async function initConfigFiles(hardware_version) {
+  await mkdir("/home/pi/PlanktoScope")
+
   await Promise.all([
     copyFile(
-      `/home/pi/PlanktoScope/default-configs/${hardware_version}.config.json`,
-      "/home/pi/PlanktoScope/config.json",
+      `/opt/PlanktoScope/default-configs/${hardware_version}.config.json`,
+      SOFTWARE_PATH,
     ),
     copyFile(
-      `/home/pi/PlanktoScope/default-configs/${hardware_version}.hardware.json`,
-      "/home/pi/PlanktoScope/hardware.json",
+      `/opt/PlanktoScope/default-configs/${hardware_version}.hardware.json`,
+      HARDWARE_PATH,
     ),
     // Create calibration.json from defaults if it doesn't exist yet.
     // Unlike config/hardware, this never overwrites — preserving user calibrations.
@@ -62,6 +65,7 @@ export async function removeConfig() {
   await Promise.all([
     rm(HARDWARE_PATH, { force: true }),
     rm(SOFTWARE_PATH, { force: true }),
+    rm(CALIBRATION_PATH, { forrce: true }),
   ])
 }
 
@@ -100,4 +104,3 @@ export async function updateCalibrationConfig(...args) {
 export async function hasCalibrationConfig() {
   return hasConfig(CALIBRATION_PATH)
 }
-
diff --git a/lib/mediamtx.js b/lib/mediamtx.js
index b6d8a1370..e05155b11 100644
--- a/lib/mediamtx.js
+++ b/lib/mediamtx.js
@@ -3,8 +3,8 @@ import os from "os"
 import { queue } from "./helpers.js"
 
 const config_template_path =
-  "/home/pi/PlanktoScope/os/mediamtx/mediamtx.template.yml"
-const config_path = "/home/pi/PlanktoScope/os/mediamtx/mediamtx.yml"
+  "/opt/PlanktoScope/os/mediamtx/mediamtx.template.yml"
+const config_path = "/opt/PlanktoScope/os/mediamtx/mediamtx.yml"
 
 async function configureMediaMTX({ hostname, address } = {}) {
   let content = await readFile(config_template_path, "utf8")
diff --git a/lib/nodered.js b/lib/nodered.js
index 8f0bb156c..854a6bc3c 100644
--- a/lib/nodered.js
+++ b/lib/nodered.js
@@ -3,7 +3,7 @@ import { createRequire } from "node:module"
 
 const require = createRequire(import.meta.url)
 
-const node_red_settings_path = "/home/pi/PlanktoScope/node-red/settings.cjs"
+const node_red_settings_path = "/opt/PlanktoScope/node-red/settings.cjs"
 
 export async function promiseDashboardOnline() {
   const { uiPort: port } = require(node_red_settings_path)
diff --git a/node-red/30-override.conf b/node-red/30-override.conf
index 3c0ac6765..25cb6dc2e 100644
--- a/node-red/30-override.conf
+++ b/node-red/30-override.conf
@@ -8,4 +8,4 @@ Before=mosquitto.service
 
 [Service]
 ExecStart=
-ExecStart=/home/pi/.local/bin/node-red-pi $NODE_OPTIONS --settings /home/pi/PlanktoScope/node-red/settings.cjs $NODE_RED_OPTIONS
+ExecStart=/home/pi/.local/bin/node-red-pi $NODE_OPTIONS --settings /opt/PlanktoScope/node-red/settings.cjs $NODE_RED_OPTIONS
diff --git a/node-red/justfile b/node-red/justfile
index aa547c05d..59334c64d 100644
--- a/node-red/justfile
+++ b/node-red/justfile
@@ -16,7 +16,7 @@ setup-dev:
 
 dev:
     -sudo systemctl stop nodered
-    node --watch-path ~/PlanktoScope/node-red/nodes/ ~/.local/bin/node-red --settings ~/PlanktoScope/node-red/settings.cjs
+    node --watch-path /opt/PlanktoScope/node-red/nodes/ ~/.local/bin/node-red --settings /opt/PlanktoScope/node-red/settings.cjs
 
 test:
     validator projects/dashboard/flows.json
diff --git a/node-red/projects/dashboard b/node-red/projects/dashboard
index 41122091e..539a102f1 160000
--- a/node-red/projects/dashboard
+++ b/node-red/projects/dashboard
@@ -1 +1 @@
-Subproject commit 41122091e7fcd49f75773e711a5b8998e6d49792
+Subproject commit 539a102f133da23d61aac34bf8e248721bd9cc3d
diff --git a/os/caddy/Caddyfile b/os/caddy/Caddyfile
index e7f07d416..6d8f16fa7 100644
--- a/os/caddy/Caddyfile
+++ b/os/caddy/Caddyfile
@@ -42,7 +42,7 @@
 
 	# We want everyrthing else /* to frontend
 	handle /* {
-        root * /home/pi/PlanktoScope/frontend/dist
+        root * /opt/PlanktoScope/frontend/dist
         try_files {path} /index.html
         file_server
 	}
diff --git a/os/image/README.md b/os/image/README.md
index c815bdc50..8af3c7182 100644
--- a/os/image/README.md
+++ b/os/image/README.md
@@ -4,9 +4,6 @@ This folder contains scripts and documentation to build the PlanktoScope OS imag
 
 The scripts should work on standard Linux installations, in case of doubt use Raspberry Pi OS.
 
-
-
-
 ## How to use
 
 ### Bootstrap Raspberry Pi OS
diff --git a/os/image/mount-firmware.service b/os/image/mount-firmware.service
index a5b5a2e2c..c673661b6 100644
--- a/os/image/mount-firmware.service
+++ b/os/image/mount-firmware.service
@@ -3,7 +3,7 @@ Description=Mount firmware partition
 
 [Service]
 Type=oneshot
-ExecStart=/home/pi/PlanktoScope/os/image/mount-firmware.js
+ExecStart=/opt/PlanktoScope/os/image/mount-firmware.js
 RemainAfterExit=yes
 
 [Install]
diff --git a/os/machine-name/generate-hostname.service b/os/machine-name/generate-hostname.service
index d5670c001..c0a3a889f 100644
--- a/os/machine-name/generate-hostname.service
+++ b/os/machine-name/generate-hostname.service
@@ -10,7 +10,7 @@ Before=sysinit.target
 
 [Service]
 Type=oneshot
-ExecStart=/home/pi/PlanktoScope/os/machine-name/generate-hostname.sh
+ExecStart=/opt/PlanktoScope/os/machine-name/generate-hostname.sh
 
 [Install]
 WantedBy=sysinit.target
diff --git a/os/machine-name/generate-machine-name.service b/os/machine-name/generate-machine-name.service
index ff953862c..3a08b99dc 100644
--- a/os/machine-name/generate-machine-name.service
+++ b/os/machine-name/generate-machine-name.service
@@ -9,7 +9,7 @@ Before=systemd-hostnamed.service
 [Service]
 Type=oneshot
 ExecStartPre=sh -c "echo 'unknown' >/run/machine-name"
-ExecStart=/home/pi/PlanktoScope/os/machine-name/generate-machine-name.sh
+ExecStart=/opt/PlanktoScope/os/machine-name/generate-machine-name.sh
 
 [Install]
 WantedBy=sysinit.target
diff --git a/os/mediamtx/justfile b/os/mediamtx/justfile
index 27a4279db..0a4a27961 100644
--- a/os/mediamtx/justfile
+++ b/os/mediamtx/justfile
@@ -1,7 +1,7 @@
 setup:
     sudo ./setup_h264_sysctl.sh
     wget https://github.com/bluenviron/mediamtx/releases/download/v1.16.2/mediamtx_v1.16.2_linux_arm64.tar.gz -P /tmp
-    wget https://raw.githubusercontent.com/bluenviron/mediamtx/refs/tags/v1.16.2/internal/servers/webrtc/reader.js -O /home/pi/PlanktoScope/frontend/src/pages/preview/reader.js
+    wget https://raw.githubusercontent.com/bluenviron/mediamtx/refs/tags/v1.16.2/internal/servers/webrtc/reader.js -O /opt/PlanktoScope/frontend/src/pages/preview/reader.js
     cd /tmp && tar -xf /tmp/mediamtx_v1.16.2_linux_arm64.tar.gz
     -sudo systemctl stop mediamtx
     sudo cp /tmp/mediamtx /usr/local/bin/mediamtx
diff --git a/os/mediamtx/mediamtx.service b/os/mediamtx/mediamtx.service
index a8d9d55cd..4314089ce 100644
--- a/os/mediamtx/mediamtx.service
+++ b/os/mediamtx/mediamtx.service
@@ -5,7 +5,7 @@ After=network.target
 Wants=network.target
 
 [Service]
-ExecStart=/usr/local/bin/mediamtx /home/pi/PlanktoScope/os/mediamtx/mediamtx.yml
+ExecStart=/usr/local/bin/mediamtx /opt/PlanktoScope/os/mediamtx/mediamtx.yml
 
 [Install]
 WantedBy=multi-user.target
diff --git a/os/preimage.sh b/os/preimage.sh
index 9ec913c28..8901ba4a4 100755
--- a/os/preimage.sh
+++ b/os/preimage.sh
@@ -18,8 +18,9 @@ rm -f "$HOME"/.gitconfig
 rm -rf "$HOME"/.ssh
 rm -rf "$HOME"/data
 rm -f "$HOME"/filebrowser.db
-rm -f "$HOME"/planktoScope/hardware.json
+rm -f "$HOME"/PlanktoScope/hardware.json
 rm -f "$HOME"/PlanktoScope/config.json
+rm -f "$HOME"/PlanktoScope/calibartion.json
 
 # Clear machine-id so that it will be regenerated on the next boot
 # This is also the condition for ConditionFirstBoot=yes
diff --git a/os/raspberry/bootloader.sh b/os/raspberry/bootloader.sh
index 925f17323..8bafbd9fc 100755
--- a/os/raspberry/bootloader.sh
+++ b/os/raspberry/bootloader.sh
@@ -12,7 +12,9 @@ cp /usr/lib/firmware/raspberrypi/bootloader-2712/latest/recovery.bin /tmp
 rpi-eeprom-config /tmp/pieeprom-2025-11-05.bin --config boot.ini --out /tmp/pieeprom.upd
 rpi-eeprom-digest -i /tmp/pieeprom.upd -o /tmp/pieeprom.sig
 
+sudo mount -o remount,rw /boot/firmware
 sudo cp /tmp/pieeprom.upd /tmp/pieeprom.sig /tmp/recovery.bin /boot/firmware/
+sudo mount -o remount,ro /boot/firmware
 
 # The bootloader will be installed on first boot and the files removed
 # see https://github.com/fairscope/PlanktoScope/pull/589
diff --git a/os/raspberry/firmware.sh b/os/raspberry/firmware.sh
index ad1299706..3b2009bc5 100755
--- a/os/raspberry/firmware.sh
+++ b/os/raspberry/firmware.sh
@@ -1,5 +1,7 @@
 #!/bin/bash -eux
 
+sudo mount -o remount,rw /boot/firmware
+
 # Configure firmware
 # https://www.raspberrypi.com/documentation/computers/config_txt.html
 sudo bash -c "cat \"config.ini\" >> \"/boot/firmware/config.txt\""
@@ -17,3 +19,5 @@ sudo bash -c "cat \"config.ini\" >> \"/boot/firmware/config.txt\""
 [ ! -f /boot/firmware/cmdline.txt ] || \
   grep -qw logo.nologo /boot/firmware/cmdline.txt || \
   sudo sed -i 's/$/ logo.nologo/' /boot/firmware/cmdline.txt
+
+sudo mount -o remount,ro /boot/firmware
diff --git a/os/raspberry/planktoscope-org.firstboot.service b/os/raspberry/planktoscope-org.firstboot.service
index ec9dd5d33..787d55450 100644
--- a/os/raspberry/planktoscope-org.firstboot.service
+++ b/os/raspberry/planktoscope-org.firstboot.service
@@ -4,7 +4,7 @@ ConditionFirstBoot=yes
 
 [Service]
 Type=oneshot
-ExecStart=/home/pi/PlanktoScope/os/raspberry/firstboot.sh
+ExecStart=/opt/PlanktoScope/os/raspberry/firstboot.sh
 
 [Install]
 WantedBy=sysinit.target
diff --git a/os/rauc/rauc.ini b/os/rauc/rauc.ini
index 46f8c7fd0..8d770aa6f 100644
--- a/os/rauc/rauc.ini
+++ b/os/rauc/rauc.ini
@@ -9,14 +9,14 @@ data-directory=/data/rauc
 # https://rauc.readthedocs.io/en/latest/using.html#system-based-customization-handlers
 [handlers]
 # https://rauc.readthedocs.io/en/latest/integration.html#custom
-bootloader-custom-backend=/home/pi/PlanktoScope/os/rauc/custom-bootloader-script
+bootloader-custom-backend=/opt/PlanktoScope/os/rauc/custom-bootloader-script
 # https://rauc.readthedocs.io/en/latest/reference.html#handlers-section
 # TODO
 # system-info=/usr/lib/raspberrypi-firmware-rauc-bootloader-backend/system-info
 
 # https://rauc.readthedocs.io/en/latest/reference.html#keyring-section
 [keyring]
-path=/home/pi/PlanktoScope/os/rauc/demo.cert.pem
+path=/opt/PlanktoScope/os/rauc/demo.cert.pem
 
 # https://rauc.readthedocs.io/en/latest/reference.html#slot-slot-class-idx-sections
 # Generated by rauc.js
diff --git a/os/setup-ci.sh b/os/setup-ci.sh
index f0ee2cc7b..8556fe0b4 100755
--- a/os/setup-ci.sh
+++ b/os/setup-ci.sh
@@ -7,10 +7,10 @@ export LANG="en_US.UTF-8"
 
 # The PlanktoScope monorepo is used for running and iterating on software components
 # https://github.com/fairscope/planktoscope
-sudo cp -r "$build_scripts_root"/.. "$HOME/PlanktoScope"
-sudo chown -R "$USER:$USER" "$HOME/PlanktoScope"
+sudo cp -r "$build_scripts_root"/.. "/opt/PlanktoScope"
+sudo chown -R "$USER:$USER" "/opt/PlanktoScope"
 
 sudo apt install -y just
-just --justfile "$HOME"/PlanktoScope/justfile
+just --justfile /opt/PlanktoScope/justfile
 ./postinstall.sh
 ./preimage.sh
diff --git a/os/setup.sh b/os/setup.sh
index 48dbe8d45..b455bcfa7 100755
--- a/os/setup.sh
+++ b/os/setup.sh
@@ -12,11 +12,13 @@ if [ "$line" != "$expected" ]; then
   exit 1
 fi
 
-cd /home/pi
 sudo apt install -y git just
+cd /opt
 if cd PlanktoScope; then
     git pull
 else
+    sudo mkdir PlanktoScope
+    sudo chown pi:pi PlanktoScope
     git clone https://github.com/fairscope/PlanktoScope.git
     cd PlanktoScope
 fi
diff --git a/segmenter/planktoscope-org.segmenter.service b/segmenter/planktoscope-org.segmenter.service
index 177370ddc..ea851b554 100644
--- a/segmenter/planktoscope-org.segmenter.service
+++ b/segmenter/planktoscope-org.segmenter.service
@@ -8,7 +8,7 @@ After=nodered.service
 Type=simple
 Environment=HOME=/home/pi
 Environment=PLANKTOSCOPE_DATA_PATH=/home/pi/data
-WorkingDirectory=/home/pi/PlanktoScope/segmenter
+WorkingDirectory=/opt/PlanktoScope/segmenter
 ExecStart=/usr/local/bin/uv run main.py
 User=pi
 Group=pi