diff --git a/scripts/mqtt_nodered.json b/flows/mqtt_nodered.json
similarity index 100%
rename from scripts/mqtt_nodered.json
rename to flows/mqtt_nodered.json
diff --git a/history_working_pi b/history_working_pi
deleted file mode 100644
index 7c84a67..0000000
--- a/history_working_pi
+++ /dev/null
@@ -1,97 +0,0 @@
-#MANUAL CONFIGURATION
-#COPY PASTE LINE BY LINE
-
- #Update and upgrade you Pi
- sudo apt-get update -y && sudo apt-get full-upgrade -y
- sudo reboot now
- 
- #Configure your Pi
- sudo raspi-config
- #Interfacing Options > Camera > Yes > OK
- #Interfacing Options > SSH > Yes > OK
- #Interfacing Options > I2C > Yes > OK
- #Interfacing Options > SSH > No > Yes > OK
- #Reboot > Yes
- 
- #Install librairies for the steppers (pump and focus)
- pip3 install adafruit-blinka
- sudo pip3 install adafruit-circuitpython-motorkit
- 
- #Install the librairy for the fan
- git clone https://github.com/WiringPi/WiringPi.git
- cd WiringPi
- sudo ./build
- sudo apt-get install gcc -y
- 
- #Install Node-Red
- cd
- sudo apt-get install build-essential -y
- bash <(curl -sL https://raw.githubusercontent.com/node-red/linux-installers/master/deb/update-nodejs-and-nodered)
- #Press y and y again to confirm the installation of Node-RED and wait.
- 
- cd .node-red/
- npm install node-red-dashboard
- npm install node-red-contrib-python3-function
- npm install node-red-contrib-camerapi
- npm install node-red-contrib-gpsd
- npm install node-red-contrib-web-worldmap
- sudo systemctl enable nodered.service
- 
-#BUILD CONFIGURATION
-#COPY PASTE BLOCK BY BLOCK
- 
- sudo pip3 install jupyter
- pip install matplotlib
- pip3 install matplotlib
- sudo apt-get install exfat-fuse -y
- sudo apt-get install exfat-utils -y
- pip install paho-mqtt
- pip3 install paho-mqtt
- sudo apt-get install mosquitto mosquitto-clients -y
- 
- 
- 
- 
- pip install -U git+https://github.com/morphocut/morphocut.git@pyrocystis
- pip3 install -U git+https://github.com/morphocut/morphocut.git@pyrocystis
- sudo pip3 install morphocut --upgrade
- pip3 install morphocut --upgrade
- pip3 uninstall morphocut
- pip uninstall morphocut
- pip uninstall -U git+https://github.com/morphocut/morphocut.git@pyrocystis
- pip freeze | xargs pip uninstall -y
- pip3 freeze | xargs pip3 uninstall -y
- sudo pip3 freeze | xargs pip3 uninstall -y
- pip3 uninstall morphocut
- sudo pip3 uninstall morphocut
- sudo pip3 install morphocut
- sudo pip3 uninstall morphocut
- pip install -U git+https://github.com/morphocut/morphocut.git@pyrocystis
- pip3 install -U git+https://github.com/morphocut/morphocut.git@pyrocystis
- 
- 
- sudo apt-get purge wolfram-engine -y
- sudo apt-get remove vlc* -y
- sudo apt-get update -y && sudo apt-get upgrade -y
- sudo apt-get install build-essential cmake pkg-config -y
- sudo apt-get install libjpeg-dev libtiff5-dev libjasper-dev libpng12-dev -y
- sudo apt-get install libavcodec-dev libavformat-dev libswscale-dev libv4l-dev -y
- sudo apt-get install libxvidcore-dev libx264-dev -y
- sudo apt-get install libgtk2.0-dev -y
- sudo apt-get install libatlas-base-dev gfortran -y
- sudo apt-get install python2.7-dev python3-dev -y
- sudo apt-get install libjpeg-dev libtiff5-dev libjasper-dev libpng-dev -y
- sudo apt-get install libfontconfig1-dev libcairo2-dev -y
- sudo apt-get install libgdk-pixbuf2.0-dev libpango1.0-dev -y
- sudo apt-get install libgtk2.0-dev libgtk-3-dev -y
- sudo apt-get install libhdf5-dev libhdf5-serial-dev libhdf5-103 -y
- sudo apt-get install libqtgui4 libqtwebkit4 libqt4-test python3-pyqt5 -y
- pip install "picamera[array]"
- pip3 install opencv-contrib-python==4.1.0.25
- 
- sudo apt-get install ffmpeg git python3-picamera python3-ws4py -y
- git clone https://github.com/waveform80/pistreaming.git
- git clone git@github.com:Lawouach/WebSocket-for-Python.git
- pip install ws4py
- pip3 install ws4py
- pip3 install pyzmq
diff --git a/morphocut/error.txt b/morphocut/error.txt
deleted file mode 100644
index 258737d..0000000
--- a/morphocut/error.txt
+++ /dev/null
@@ -1,72 +0,0 @@
-#test using python3.7 morphocut.py
-Processing images under /home/pi/Desktop/PlanktonScope_acquisition/01_16_2020/15...
-0it [00:00, ?it/s]
-0it [00:00, ?it/s]Found 94 files in /home/pi/Desktop/PlanktonScope_acquisition/01_16_2020/15.
-
-Object 35_41_180124_84: : 85it [00:17,  5.95it/s]
-Frame 35_41_180124: : 1it [00:17, 17.03s/it]
-Object 35_41_763395_168: : 169it [00:24, 47.97it/s]
-Frame 35_41_763395: : 2it [00:24, 14.11s/it]
-Object 35_42_339153_245: : 245it [00:31, 44.73it/s]
-Frame 35_42_339153: : 3it [00:31, 11.93s/it]
-Object 35_42_899894_320: : 319it [00:38, 42.28it/s]
-Frame 35_42_899894: : 4it [00:38, 10.44s/it]
-Object 35_43_467613_394: : 394it [00:45, 44.59it/s]
-Frame 35_43_467613: : 5it [00:44,  9.36s/it]
-Object 35_44_040639_465: : 466it [00:56, 32.28it/s]
-Frame 35_44_040639: : 6it [00:59,  9.95s/it]
-Object 35_44_040639_465: : 466it [00:59,  7.78it/s]
-Traceback (most recent call last):
-  File "/home/pi/Downloads/Morphocut.py", line 115, in <module>
-    p.run()
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 748, in run
-    for _ in self.transform_stream():
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/stream.py", line 68, in transform_stream
-    for obj in progress:
-  File "/home/pi/.local/lib/python3.7/site-packages/tqdm/std.py", line 1104, in __iter__
-    for obj in iterable:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/contrib/ecotaxa.py", line 111, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/stream.py", line 184, in transform_stream
-    for i, obj in enumerate(stream, start=self.start):
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/image.py", line 142, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/stream.py", line 68, in transform_stream
-    for obj in progress:
-  File "/home/pi/.local/lib/python3.7/site-packages/tqdm/std.py", line 1104, in __iter__
-    for obj in iterable:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
-    for obj in stream:
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 492, in transform_stream
-    result = self.transform(*parameters)  # pylint: disable=no-member
-  File "/home/pi/.local/lib/python3.7/site-packages/morphocut/image.py", line 78, in transform
-    image, in_range=in_range, out_range=self.out_range
-  File "/home/pi/.local/lib/python3.7/site-packages/skimage/exposure/exposure.py", line 352, in rescale_intensity
-    image = (image - imin) / float(imax - imin)
-MemoryError
diff --git a/pipeline/focus.py b/pipeline/focus.py
deleted file mode 100644
index 837ec79..0000000
--- a/pipeline/focus.py
+++ /dev/null
@@ -1,54 +0,0 @@
-#!/usr/bin/env python
-from adafruit_motor import stepper
-from adafruit_motorkit import MotorKit
-from time import sleep
-
-from thread2 import Thread
-import sys
-
-nb_step = int(sys.argv[1])
-orientation = str(sys.argv[2])
-toogler = str(sys.argv[3])
-
-
-#Execute a python cmd with the previous defined variables from php
-
-
-kit = MotorKit()
-
-stage = kit.stepper1
-
-stage.release()
-
-def focus(steps,orientation):
-    #0.25mm/step
-    #31um/microsteps
-
-    stage.release()
-    
-    if orientation == 'up':
-        for i in range(steps):
-            stage.onestep(direction=stepper.FORWARD, style=stepper.MICROSTEP)
-            sleep(0.001)
-            
-    if orientation == 'down':
-        for i in range(steps):
-            stage.onestep(direction=stepper.BACKWARD, style=stepper.MICROSTEP)
-            sleep(0.001)
-            
-    stage.release()
-
-focus_thread = Thread(target = focus, name = 'focus_thread', args =(nb_step, orientation) )
- 
-if toogler == "ON":
-        
-    focus_thread.start()
-    focus_thread.isAlive()
-    
-if toogler == "OFF":
-        
-    focus_thread.terminate()
-    focus_thread.join()
-    focus_thread.isAlive()
-    stage.release()
-
diff --git a/pipeline/pump.py b/pipeline/pump.py
deleted file mode 100644
index 52b0e68..0000000
--- a/pipeline/pump.py
+++ /dev/null
@@ -1,41 +0,0 @@
-from adafruit_motor import stepper
-from adafruit_motorkit import MotorKit
-from time import sleep
-
-import sys
-
-vol = int(sys.argv[1])
-flowrate = float(sys.argv[2])
-dir = str(sys.argv[3])
-
-kit = MotorKit()
-
-pump_stepper = kit.stepper2
-
-pump_stepper.release()
-
-def pump(vol, flowrate, dir):
-    
-    if dir == "foward":
-        dir=stepper.FORWARD
-    if dir == "backward":
-        dir=stepper.BACKWARD
-        
-    nb_step=vol*507 #if sleep(0.05) in between 2 steps
-    #35000steps for 69g
-    
-    #nb_step=vol*460 if sleep(0) in between 2 steps
-    duration=(vol*60)/flowrate
-    
-    delay=(duration/nb_step)-0.005
-    
-    for i in range(nb_step):
-        pump_stepper.onestep(direction=dir, style=stepper.DOUBLE)
-        sleep(delay)
-        
-    sleep(1)
-    pump_stepper.release()
-    
-#volume, flowrate (from 0 to 20), direction (foward or backward)
-pump(vol, flowrate, dir)
-
diff --git a/pipeline/settings_web_interface.sh b/pipeline/settings_web_interface.sh
deleted file mode 100644
index 89dc38d..0000000
--- a/pipeline/settings_web_interface.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-
-cd ~
-sudo touch starting.sh
-sudo chmod 777 starting.sh
-sudo echo 'sudo chmod 777 /dev/i2c-1' >> starting.sh
-
-sudo echo './starting.sh' >> .bashrc
-
-sudo reboot
diff --git a/scripts/daemon.zip b/scripts/daemon.zip
deleted file mode 100644
index babd17e..0000000
Binary files a/scripts/daemon.zip and /dev/null differ
diff --git a/scripts/kill_image.sh b/scripts/kill_image.sh
deleted file mode 100644
index 72b021d..0000000
--- a/scripts/kill_image.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/bash    
-
-#In order to kill an on going acquisition, type this command
-#bash $HOME/PlanktonScope/scripts/kill_image.sh image.py in_path sample_project sample_id acq_id
-
-path=$1
-
-kill -9 `ps ax | grep "image.py" | head -1 | awk '{print $1}'`
-kill -9 `ps ax | grep "image.py" | head -1 | awk '{print $1}'`
-
-rm -r $path
diff --git a/scripts/killer.sh b/scripts/killer.sh
deleted file mode 100644
index 99fee90..0000000
--- a/scripts/killer.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash    
-#Run this script using this type of command line : bash killer.sh name_of_the_python_script_to_kill.py
-
-scrip_name=$1
-
-kill -9 `ps ax | grep "$scrip_name" | head -1 | awk '{print $1}'`
-
-python3.7 $HOME/PlanktonScope/scripts/recover.py