[TOC]
Config.py : Parameters of each device (Printer,Wells,Valve, etc.). Read it before using any program to be sure that the parameters correspond to your devices. You can change their values but don't change the name of the variables. You can add new variables if you need to. To call a variable in an other script you have to:
- import Config (if your script is in the same deposit as the file Config.py)
- write your variable like this : Config.$NameOfYourVariable"
Driver.py : System tested: Windows(10)+Linux(PopOS) Works with:Python 3.8;3.7
Communication method : serial (package pyserial)
Drivers for the 3D-mill. Define a class called CNC design for the control of the 3D printer. It contains all the basic methods to communicate with the device. Those methods are used in the script Wells.py.
Methods in Driver.py :
- Open/Close Connection (Open or close the communication with the device)
- Status (Get the current state of the device)
- WaitForIdle (Wait until the device has finished his action)
- Move (Move the device to target coordinates)
Wells.py : System tested: Windows(10)+Linux(PopOS) Works with:Python 3.8;3.7
Program to move the 3D-mill to specific wells (on a eppendorf rack). This script uses the class CNC created in Driver.py to move the 3d-mill. A class Wells is created with the following methods :
- Wells_1 (Ask the user if the 3D-mill is above the Wells 1)
- CoordWells (Calculate the coordinates of the wells)
- MoveWells (Move to the wells depending of the number given by the user)
- CheckValue (Check if the value of the wells give by the user is correct)
**log_file **: Historic of the instructions sent to the 3D-mill. If the printer seems to not work when u send a list of instructions, check the file to be sure there is not a problem with your script. For example if you open twice the communication with the device.
More information can be found at python/Python Program/3D Printer Control
Valve.py : System tested:Windows(10)+Linux(PopOS) Works with:Python 3.8
Communication method : serial (package pyserial)
Defines a class Valve that contains all the methods to interact with one or more valve (in daisy chain). Methods in Valve:
- Open Connection (Open the communication with the device)
- Status (Get the current state of the device)
- WaitForIdle (Wait until the device has finished his action)
- ValveRotation (Rotate the valve to target position)
More information python/Python Program/Hamilton valve/How_to_use.md
DriverMS2000.py: System Tested:Windows(10) Works with:Python 3.8
Communication method : serial (package pyserial)
Drivers for the translation plate (MS2000). Contains a class called MS2000 containing all the methods needed to communicate with the device and to save the positions of the selected ROIs.
Methods in MS2000:
- Open/Close Connection (Open or close the communication with the device)
- Status (Get the current state of the device)
- WaitForIdle (Wait until the device has finished its action)
- MoveREL (Move the device to target coordinates in relative coordinates)
- MoveABSOL (Move the device to target cooridnates in absolute coordinates)
- AxisPosition (Return the current axis positions of the device)
- MemorizeROI (Save the coordinates of a ROI)
- GoToROI (Move to all the ROI saved before)
- Speed (Set the speed of the device)
- Brightness (Set the luminosity of the device - in case there is a LED system attached to the stage, like on the merFISH setup)
More detailed information can be found python/Python Program/ASI MS2000 translation stage/How_to_use.md
andorEmccd.py : System Tested:Windows(10) Works with:Python 3.6;3.7 Doesn't work with:Python 3.8
Communication method : need to download and install the emCCD libraries (atmcd32d.dll or atmcd64d.dll) provided by ANDOR
The initial examples where found here. Depending on whether the system if 32bit or 64bit, the program will use different libraries for the camera (either atmcd32d.dll or atmcd64d.dll). Before starting, make sure that the drivers are properly installed and can be found at the location indicated in the program (see andorEmccd.py, line 52).
Contains the methods to interact with the Andor camera, acquire data and more. All the methods are called from the dll library and are defined/described in the SDK manual. The original script andorEmccd.py was modified by Aymerick :
- The internal shutter was not working. It is fixed now.
- A get_status method was added
- Aset_spool method was added.
Check the script example.py to understand how to use this class. More information can be found python/Python Program/Andor emCCD/How_to_use.md
Problem : File where you can find some solutions to some problems I have encountered during the developement of this scripts
control_celesta.py : System Tested:Windows(10)+Linux (PopOs) Works with:Python 3.8
Communication method : Python communicates with the Celesta through an RG45 cable
Celesta : Folder that contains current development regarding the control of the Celesta Engine Light.
One of the files was created by Bogdan Bintu to control their Celesta through an RG45 cable, it is called "celesta.py". It was used as a base to control our own. The code called "control_celesta.py" will be used to modulate the lasers in sync with the camera ORCA Flash 4.0 (Hamamatsu) and the filter wheel Lambda 10-3 (Sutter Instruments).
daq.py : System Tested:Xubuntu Works with:Python 3.7
Communication method : In order to communicate with the Measurement Computing acquisition card, a universal library for Linux is available on gitHub here. As usual, this library is actually written in C/C++ and an API (Application Programming Interface) is used to interact directly with this library in Python.
Note that all files and documentation can be found python/Python Program/Measurement_computing_DAQ/Libraries. The installation procedure works in two steps :
- Installation of the uldaq library and C/C++ compilers : Follow the instructions described here. Make sure you are running the latest version, else it might not be compatible with your version of Python.
- Installation of the uldaq API for Python and test of the DAQ : The information regarding the installation are here. Installation must be performed in the local environment. The first example analyzed was the function d_in.py that is reading the first available digital port. The function is analyzed in the following python files daq.py and daq_experiment.py.
All files were installed python/Python Program/Thorlabs camera DCC1545/Doc. A manual of all the cameras can be also be found in the same folder.
The CMOS camera from Thorlabs was tested on the computer. This model is monochrome with a 1280x1024 pixels sensor. The SDK/ C/C++ libraries for Linux can be found here.
In order to install a Python wrapper, the following sdk needs to be installed as well. Follow theses instruction:
- move to your Python/Conda virtual environment
- cd to the folder containing the Python wrapper (for this computer it is located [here](python/Python Program/Thorlabs camera DCC1545/Doc/Scientific_Camera_Interfaces_Linux-1.3/Python_SDK)
- run
python -m pip install thorlabs_tsi_camera_python_sdk_package.zip
Installation went well though in the end it was impossible to detect any camera on the computer... apparently this model of camera is not supported.
Since our DCC-1545 camera was not detected using the Thorlab sdk, another methods was described in the (python/Python Program/Thorlabs camera DCC1545/Doc/DCU223C-Manual.pdf), p.61. Following the link indicated for Linux, it is possible to download the Linux drivers for the camera (see python/Python Program/Thorlabs camera DCC1545/Doc/uEye_Linux_382_64Bit/uEye_Linux_382_64Bit/ for the drivers).
Following the readme file, install the uEye SDK for Linux. In order to check if the installation worked :
- start a new terminal with super-user right
- Use the following command to start the Daemon :
/etc/init.d/ueyeusbdrc start - In order to test whether there is a camera connected to the PC, type
ueyesetid -d. If there is a camera, the device should appear with the right serial #. Interestingly, the model of camera is not DCC1545 but UI-1540ME-M and can be found directly on the IDS (imaging development systems Gmbh) website. - In order to close the program type :
/etc/init.d/ueyeusbdrc stop.
A specific API to interface uEye with Python can be downloaded here. In order to found the manual and examples, you need to download the files available on the webpage. A very simple example can also be downloaded from the IDS website and can be found in the folder python/Python Program/Thorlabs camera DCC1545/Doc/pyueye/uEye_SimpleLive_PyuEye_OpenCV. It was tested and allow for a proper detection of the DCC1545 camera.
Finally, the manual with all the functions can be found here but you need to have an account to access this webpage.
PIController.py: System Tested:Windows(10) Works with:Python 3.8 PI Tested:C-663
Comunication method : (USB). Need to install pipython by using the CD.
Drivers for the PI stepper motor controller. Contains a class called PITranslationStage containing all the methods needed to communicate with the device.
Methods in PIController:
- Open/Close Connection (Open or close the communication with the device)
- WaitForIdle (Wait until the device has finished his action)
- Move (Move the device to target coordinates in absolute coordinates)
- Position (Return the current axis positions of the device)
More detailed information can be found python/Python Program/PI stepper motor controller/README_PIController.md
Hamamatsu_camera.py: System Tested:Windows(10) Works with:Python 3.7 - Camera tested from the RAMM setup with Spyder
The program is using the SDK4 from Hamamatsu website. The program is using the C dll and a complete documentation can be found when downloading the SDK. The initial program was downloaded from Zhuang lab github and was modified for the test.
Problem : for some reason the program cannot run twice in a row. Between each test Spyder must be close, else an error message is sent. For the moment, no correction seems to work.