Track C.elegans and light single C.elegans inside microscope by LCD projector. This project is code by PyQt5 and Python2 in anaconda, which is tested on Archlinux.
~~~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| | | | | User Interface: | | |
| | | | | 1. Show Image | | Project |
| | \ | | \ | 2. Select ROI | \ | image |
| Camera: |-----\ | Andor |----\ | 3. Set Parameters|----\ | into |
|Andor Zyla|-----/ | SDK3 |----/ | --------------- |----/ | Microscope |
| (5.2) | / | | / | Calculation: | / | |
| | | | | Generate image | | |
~~~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~- Install Andor SDK3 in ArchLinux or Deepin
# Andor sdk3 only run below linux kernel 4, so I install linux kernel 3.16
# Prepare tool for kenel compile from AUR in ArchLinux
sudo pacman -S linux-headers numactl
yaourt linux-lts316
# Mannual download kernel tar and compile with standard procedure
wget https://cdn.kernel.org/pub/linux/kernel/v3.x/linux-3.16.79.tar.xz
unxz -v linux-3.16.79.tar.xz
wget https://cdn.kernel.org/pub/linux/kernel/v3.x/linux-3.16.79.tar.sign
gpg --verify linux-3.16.79.tar.sign
gpg --recv-keys <public key>
tar xvf linux-3.16.79.tar
cd linux-3.16.79
cp -v /boot/config-$(uname -r) .config
sudo apt-get install build-essential libncurses-dev bison flex libssl-dev libelf-dev
make menuconfig
make -j 4
make modules_install
make install
# Update grub to boot kernel 3.16 as default(optinal)
vim /etc/default/grub
GRUB_DEFAULT="Advanced options for Deepin 15.11 GNU/Linux>Deepin 15.11 GNU/Linux, with Linux 3.16.79"
# Enter bitflow dir to install bitflow module
cd ./bitflow
./install # it will recompile bitflow.ko
vim .bashrc
export BITFLOW_INSTALL_DIRS=/home/qblab/Bin/Andor_Linux/bitflow
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/qblab/Bin/Andor_Linux/bitflow/64b/lib
# Enter the andor directory and run
sudo ./install_andor
# Then I add the follow configure to /etc/systemd/system
# andorcameralink.service
[Unit]
Description= Andor Camera Link
[Service]
ExecStart=/home/igem/Bin/andor/andorsetting.sh
[Install]
WantedBy=multi-user.targetThe andorsetting.sh is
#!/bin/sh
sudo modprobe v4l2_common
#sudo modprobe v4l1_compat
sudo modprobe videodev
sudo insmod /usr/local/mod/bitflow.ko fwDealy1=200 customFlags=1
sudo chmod a+rw /dev/video*The andorcameralink.service is enable by
systemctl enable andorcameralink.serviceAdd the nopat kernel option to the bootloader by editing /etc/default/grub, adding nopat to the line GRUB_CMDLINE_LINUX_DEFAULT and running sudo update-grub. You can check that the option is active by printing out /proc/cmdline, if it is not not the case, reboot your computer.
The official examples can run.
All software run but show AT_ERR_NODATA during live, I switch PCI slot and close C-state in DELL bios. Finally work!
- Compilation and installatin of Lima
- Dependents
sudo pacman -S python-sip
sudo pip install numpy - Compilation
# generate config.inc
make
# Edit the configuration file config.inc
...
COMPILE_CORE=1
COMPILE_ANDOR3=1
COMPILE_TIFF_SAVING=1
COMPILE_HDF5_SAVING=1
...
# Configure all python modules
make config
# Finally compile all C++ libraries
make
# Compile all Python modules
make -C sip -j3- Installation
sudo make install
# Update environment for python and library paths
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<my-new-install-dir>/Lima/lib
export PYTHONPATH=$PYTHONPATH:<my-new-install-dir>- Install Micro-manager In ArchLinux, following office document and commit from micromanager AUR
In deepin 15.11, hadim have coded a great mm build script. Only little modification are required.
- PyQtGraph
- PyQtGraph API
- Lima with andor sdk3
- Andor sdk3 Micro-manager
- Andor install guide from Libuca
- ERR11: AT_ERR_NODATA
- How to compile and install Linux Kernel 5.4.1 from source code
GNU General Public License v3.0
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