Light-sheet Dataset EXploration and Processing
Project description
DEXP
Dataset Exploration and Processing Tool
DEXP let's you view both ClearControl and Zarr formats, and copy (convert) from ClearControl format to Zarr. You can select channels and slice which lets you crop arbitrarily in time and space. You can also query information for both formats.
DEXP ZARR storage supports both directory and zip storage and different compression codecs. Expect a typicall factor 3 compression for raw data, 10x compression for deconvolved and/or denoised data, and up to 90x compression for sparse expression. Substracting the backgroundlight level (~ around 100 for sCMOS cameras) brings compression from typically 3X on raw data to almost 10x.
DEXP currently supports fusion, registration, deconvolution, isonet, vieweing with napari, volumetric rendering, video compositing (merging channels), video export to mp4, export to tiff.
DEXP should be run ideally on very fast machines very close to the storage.
Prerequisites:
Install Anaconda: https://www.anaconda.com/distribution/
On windows, make sure to insatll CUDA 10.2 (exactly that version for the current version of dexp)
Installation:
Prerequisites:
Install CUDA and other libraries
The following instructions are for Ubuntu 20.04 (recomended!)
Remove all existing CUDA and NVIDIA packages:
sudo apt-get -y purge nvidia*
sudo apt-get -y autoremove
sudo apt-get -y autoclean
sudo rm -rf /usr/local/cuda*
sudo apt-get clean
Install CUDA 11.1:
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
sudo mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/7fa2af80.pub
sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"
sudo apt-get update
sudo apt-get -y install cuda=11.1.0-1
Install CUDA 11.2:
It is recomeneded to install the most recent packages that are still compatible with CUPY and its dependencies. As of Feb 2021, this is a good choice:
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
sudo mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
wget https://developer.download.nvidia.com/compute/cuda/11.2.0/local_installers/cuda-repo-ubuntu2004-11-2-local_11.2.0-460.27.04-1_amd64.deb
sudo dpkg -i cuda-repo-ubuntu2004-11-2-local_11.2.0-460.27.04-1_amd64.deb
sudo apt-key add /var/cuda-repo-ubuntu2004-11-2-local/7fa2af80.pub
sudo apt-get update
sudo apt-get -y install cuda=11.2.0-1
Install cutensor:
sudo add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"
sudo apt-key adv --fetch-keys http://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/7fa2af80.pub
sudo apt update
sudo apt -y remove libcutensor1 libcutensor-dev libcutensor-doc
sudo apt -y install libcutensor1 libcutensor-dev libcutensor-doc
Install nccl for CUDA 11.1:
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
sudo mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/7fa2af80.pub
sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"
sudo apt-get update
sudo apt -y remove libnccl2 libnccl-dev
sudo apt -y install libnccl2=2.8.4-1+cuda11.1 libnccl-dev=2.8.4-1+cuda11.1
Install nccl for CUDA 11.2:
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
sudo mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/7fa2af80.pub
sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"
sudo apt-get update
sudo apt -y remove libnccl2 libnccl-dev
sudo apt -y install libnccl2=2.8.4-1+cuda11.2 libnccl-dev=2.8.4-1+cuda11.2
Install cudnn for CUDA 11.1:
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
sudo mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/7fa2af80.pub
sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"
sudo apt-get update
sudo apt-get -y remove libcudnn8
sudo apt-get -y install libcudnn8=8.1.0.77-1+cuda11.1
Install cub:
Nothing to do...
Another way to install CUDA and other libraries:
If you want to target CUDA 11.2:
conda install -c conda-forge cudatoolkit=11.2
conda install -c conda-forge cudnn
conda install -c conda-forge cutensor
If you want to target CUDA 11.1:
conda install -c conda-forge cudatoolkit=11.1
conda install -c conda-forge cudnn
conda install -c conda-forge cutensor
Important: tell CUPY to use cub and cutensor:
To benefit from the cub and cutensor libraries, set this env variable:
CUPY_ACCELERATORS=cub,cutensor
This can be done by opening the file: /etc/environment, and adding the line:
CUPY_ACCELERATORS="cub,cutensor"
Build/Install CUPY for CUDA 11.1:
It is recomended to install cupy using the available wheels, you must have installed the correct CUDA packages for the correct version (11.1) as detailed above. Once ready you do:
pip install cupy-cuda111==9.0.0b2
DEXP setup:
Clone dexp:
git clone https://github.com/royerlab/dexp.git
Create conda environment:
conda create --name dexp python=3.8
Activate environment:
conda activate dexp
Install dexp:
cd dexp
pip install -e .
Usage:
Always make sure that you are in the correct environment:
source activate dexp
DEXP commands:
There is currently 16 dexp commands:
Usage: dexp [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
Commands:
add
check
copy
deconv
deskew
fuse
info
isonet
serve
speedtest
stabilize
tiff
view
Sytorage info & manipulation commands: info check copy add
Lightsheet data processing commands: deskew fuse deconv stabilize isonet
Network commands: serve
Video rendering commands: render blend stack mp4
Export commnads: tiff
Viewing commands (opens napari): view
Miscellaneous: speedtest
info:
Collects information about a given dataset:
Usage: dexp info [OPTIONS] [INPUT_PATHS]...
Options:
--help Show this message and exit.
check:
Checks the integrity of a dataset:
sage: dexp check [OPTIONS] [INPUT_PATHS]...
Options:
-c, --channels TEXT List of channels, all channels when ommited.
--help Show this message and exit.
view:
Views a dataset with napari
Usage: dexp view [OPTIONS] INPUT_PATH
Opens dataset for viewing using napari.
Options:
-c, --channels TEXT list of channels, all channels when ommited.
-s, --slice TEXT dataset slice (TZYX), e.g. [0:5] (first five stacks)
[:,0:100] (cropping in z).
-v, --volume to view with volume rendering (3D ray casting)
--help Show this message and exit.
copy:
Copies a dataset from one file/folder to another file/folder. The destination is always in ZARR format (dir ort zip). Prefer 'zip' for fully processed datasets (<200GB) to be able to convenienytly copy a single file instead of a gazillion files.
Usage: dexp copy [OPTIONS] [INPUT_PATHS]...
Options:
-o, --output_path TEXT
-c, --channels TEXT List of channels, all channels when ommited.
-s, --slicing TEXT Dataset slice (TZYX), e.g. [0:5] (first five
stacks) [:,0:100] (cropping in z)
-st, --store TEXT Zarr store: ‘dir’, ‘ndir’, or ‘zip’ [default:
dir]
-z, --codec TEXT Compression codec: zstd for ’, ‘blosclz’,
‘lz4’, ‘lz4hc’, ‘zlib’ or ‘snappy’ [default:
zstd]
-l, --clevel INTEGER Compression level [default: 3]
-w, --overwrite Forces overwrite of target [default: False]
-wk, --workers INTEGER Number of worker threads to spawn. [default:
-1]
-wkb, --workersbackend TEXT What backend to spawn workers with, can be
‘loky’ (multi-process) or ‘threading’ (multi-
thread) [default: threading]
-ck, --check TEXT Checking integrity of written file. [default:
True]
--help Show this message and exit.
add:
Adds a channel from one dataset to another (possibly not yet existant) ZARR file/folder. Channels can be renamed as they are copied.
Usage: dexp add [OPTIONS] [INPUT_PATHS]...
Options:
-o, --output_path TEXT
-c, --channels TEXT List of channels, all channels when ommited.
-rc, --rename TEXT You can rename channels: e.g. if channels are
‘channel1,anotherc’ then ‘gfp,rfp’ would rename the
‘channel1’ channel to ‘gfp’, and ‘anotherc’ to ‘rfp’
-st, --store TEXT Zarr store: ‘dir’, ‘ndir’, or ‘zip’ [default: dir]
-w, --overwrite Forces overwrite of target [default: False]
--help Show this message and exit.
Deskew:
Usage: dexp deskew [OPTIONS] [INPUT_PATHS]...
Options:
-o, --output_path TEXT
-c, --channels TEXT list of channels for the view in standard
order for the microscope type (C0L0, C0L1,
C1L0, C1L1,...)
-s, --slicing TEXT dataset slice (TZYX), e.g. [0:5] (first five
stacks) [:,0:100] (cropping in z)
-st, --store TEXT Zarr store: ‘dir’, ‘ndir’, or ‘zip’
[default: dir]
-z, --codec TEXT compression codec: ‘zstd’, ‘blosclz’, ‘lz4’,
‘lz4hc’, ‘zlib’ or ‘snappy’
-l, --clevel INTEGER Compression level [default: 3]
-w, --overwrite to force overwrite of target [default:
False]
-zl, --zerolevel INTEGER ‘zero-level’ i.e. the pixel values in the
restoration (to be substracted) [default:
110]
-ch, --cliphigh INTEGER Clips voxel values above the given value, if
zero no clipping is done [default: 1024]
-dhs, --dehaze_size INTEGER Filter size (scale) for dehazing the final
regsitered and fused image to reduce effect
of scattered and out-of-focus light. Set to
zero to deactivate. [default: 65]
-ddt, --dark_denoise_threshold INTEGER
Threshold for denoises the dark pixels of
the image -- helps increase compression
ratio. Set to zero to deactivate. [default:
0]
-k, --workers INTEGER Number of worker threads to spawn, if -1
then num workers = num devices [default:
-1]
-wkb, --workersbackend TEXT What backend to spawn workers with, can be
‘loky’ (multi-process) or ‘threading’
(multi-thread) [default: threading]
-d, --devices TEXT Sets the CUDA devices id, e.g. 0,1,2 or
‘all’ [default: 0]
-ck, --check TEXT Checking integrity of written file.
[default: True]
--help Show this message and exit.
Fusion (& registration):
Fuses and registers stacks acquired on a multi-view lightsheet microscope. Right now we have only support for SimView type lightsheet microscope with 2 detection arms and 2 illmination arms. Channels must be named: 'C0L0', 'C0L1', 'C1L0', 'C1L1'. The result has a single channel called 'fused'.
Usage: dexp fuse [OPTIONS] [INPUT_PATHS]...
Options:
-o, --output_path TEXT
-c, --channels TEXT list of channels for the view in standard
order for the microscope type (C0L0, C0L1,
C1L0, C1L1,...)
-s, --slicing TEXT dataset slice (TZYX), e.g. [0:5] (first five
stacks) [:,0:100] (cropping in z)
-st, --store TEXT Zarr store: ‘dir’, ‘ndir’, or ‘zip’
[default: dir]
-z, --codec TEXT compression codec: ‘zstd’, ‘blosclz’, ‘lz4’,
‘lz4hc’, ‘zlib’ or ‘snappy’
-l, --clevel INTEGER Compression level [default: 3]
-w, --overwrite to force overwrite of target [default:
False]
-m, --microscope TEXT Microscope objective to use for computing
psf, can be: simview or mvsols [default:
simview]
-eq, --equalise / -neq, --no-equalise
Equalise intensity of views before fusion,
or not. [default: True]
-eqm, --equalisemode TEXT Equalisation modes: compute correction
ratios only for first time point: ‘first’ or
for all time points: ‘all’. [default:
first]
-zl, --zerolevel INTEGER ‘zero-level’ i.e. the pixel values in the
restoration (to be substracted) [default:
110]
-ch, --cliphigh INTEGER Clips voxel values above the given value, if
zero no clipping is done [default: 1024]
-f, --fusion TEXT Fusion mode, can be: ‘tg’ or ‘dct’.
[default: tg]
-fbs, --fusion_bias_strength <FLOAT FLOAT>...
Fusion bias strength for illumination and
detection ‘fbs_i fbs_d’, set to ‘0 0’) if
fusing a cropped region [default: 0.5,
0.02]
-dhs, --dehaze_size INTEGER Filter size (scale) for dehazing the final
regsitered and fused image to reduce effect
of scattered and out-of-focus light. Set to
zero to deactivate. [default: 65]
-ddt, --dark_denoise_threshold INTEGER
Threshold for denoises the dark pixels of
the image -- helps increase compression
ratio. Set to zero to deactivate. [default:
0]
-zpa, --zpadapodise <INTEGER INTEGER>...
Pads and apodises the views along z before
fusion: ‘pad apo’, where pad is a padding
length, and apo is apodisation length, both
in voxels. If pad=apo, no original voxel is
modified and only added voxels are apodised.
[default: 8, 96]
-lr, --loadreg Turn on to load the registration parameters
from a previous run [default: False]
-wri, --warpregiter INTEGER Number of iterations for warp registration
(if applicable). [default: 4]
-mc, --minconfidence FLOAT Minimal confidence for registration
parameters, if below that level the
registration parameters for previous time
points is used. [default: 0.3]
-md, --maxchange FLOAT Maximal change in registration parameters,
if above that level the registration
parameters for previous time points is used.
[default: 16]
-hd, --hugedataset Use this flag to indicate that the the
dataset is _huge_ and that memory allocation
should be optimised at the detriment of
processing speed. [default: False]
-k, --workers INTEGER Number of worker threads to spawn, if -1
then num workers = num devices [default:
-1]
-wkb, --workersbackend TEXT What backend to spawn workers with, can be
‘loky’ (multi-process) or ‘threading’
(multi-thread) [default: threading]
-d, --devices TEXT Sets the CUDA devices id, e.g. 0,1,2 or
‘all’ [default: 0]
-ck, --check TEXT Checking integrity of written file.
[default: True]
--help Show this message and exit.
Deconvolution:
Deconvolves stacks using a simulated PSF. Right now we only support the optics of our SimVew type light sheet (0.8 NA objectives wth custom magnfication.)
Usage: dexp deconv [OPTIONS] [INPUT_PATHS]...
Options:
-o, --output_path TEXT
-c, --channels TEXT list of channels, all channels when ommited.
-s, --slicing TEXT dataset slice (TZYX), e.g. [0:5] (first five
stacks) [:,0:100] (cropping in z)
-st, --store TEXT Zarr store: ‘dir’, ‘ndir’, or ‘zip’ [default:
dir]
-z, --codec TEXT compression codec: ‘zstd’, ‘blosclz’, ‘lz4’,
‘lz4hc’, ‘zlib’ or ‘snappy’ [default: zstd]
-l, --clevel INTEGER Compression level [default: 3]
-w, --overwrite to force overwrite of target [default: False]
-cs, --chunksize INTEGER Chunk size for tiled computation [default:
512]
-m, --method TEXT Deconvolution method: for now only lr (Lucy
Richardson) [default: lr]
-i, --iterations INTEGER Number of deconvolution iterations. More
iterations takes longer, will be sharper, but
might also be potentially more noisy depending
on method. The default number of iterations
depends on the other parameters, in particular
it depends on the choice of backprojection
operator. For ‘wb’ as little as 3 iterations
suffice.
-mc, --maxcorrection INTEGER Max correction in folds per iteration. By
default there is no limit
-pw, --power FLOAT Correction exponent, default for standard LR
is 1, set to >1 for acceleration. [default:
1.0]
-bs, --blindspot INTEGER Blindspot based noise reduction. Provide size
of kernel to use, must be an odd number:
3(recommended), 5, 7. 0 means no blindspot.
[default: 0]
-bp, --backprojection TEXT Back projection operator, can be: ‘tpsf’
(transposed PSF = classic) or ‘wb’ (Wiener-
Butterworth = accelerated) [default: tpsf]
-obj, --objective TEXT Microscope objective to use for computing psf,
can be: nikon16x08na or olympus20x10na
[default: nikon16x08na]
-dxy, --dxy FLOAT Voxel size along x and y in microns [default:
0.485]
-dz, --dz FLOAT Voxel size along z in microns [default: 1.94]
-sxy, --xysize INTEGER PSF size along xy in voxels [default: 31]
-sz, --zsize INTEGER PSF size along z in voxels [default: 31]
-d, --downscalexy2 TEXT Downscales along x and y for faster
deconvolution (but worse quality of course)
-k, --workers INTEGER Number of worker threads to spawn, if -1 then
num workers = num devices [default: -1]
-wkb, --workersbackend TEXT What backend to spawn workers with, can be
‘loky’ (multi-process) or ‘threading’ (multi-
thread) [default: threading]
-d, --devices TEXT Sets the CUDA devices id, e.g. 0,1,2 or ‘all’
[default: 0]
-ck, --check TEXT Checking integrity of written file. [default:
True]
--help Show this message and exit.
Isonet:
Provides support for Isonet deep learning based axial deconvolution: https://arxiv.org/abs/1704.01510
Usage: dexp isonet [OPTIONS] [INPUT_PATHS]...
Options:
-o, --output_path TEXT
-s, --slicing TEXT dataset slice (TZYX), e.g. [0:5] (first five
stacks) [:,0:100] (cropping in z)
-st, --store TEXT Zarr store: ‘dir’, ‘ndir’, or ‘zip’ [default:
dir]
-z, --codec TEXT compression codec: ‘zstd’, ‘blosclz’, ‘lz4’,
‘lz4hc’, ‘zlib’ or ‘snappy’ [default: zstd]
-l, --clevel INTEGER Compression level [default: 3]
-w, --overwrite to force overwrite of target [default: False]
-c, --context TEXT IsoNet context name [default: default]
-m, --mode TEXT mode: 'pta' -> prepare, train and apply, 'a' just
apply [default: pta]
-e, --max_epochs INTEGER to force overwrite of target [default: 50]
-ck, --check TEXT Checking integrity of written file. [default:
True]
--help Show this message and exit.
Video commands
DEXP has a series of video commands that let you render datasets and compose complex videos:
Usage: video [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
Commands:
blend
mp4
projrender
stack
volrender
Volume rendering:
Simple but effective volume rendering. By default should produce nice rotating views, but lots of parameters can be configured! This command produces video frames as individual PNG files in a subfolder (frames). To make a movie, blend channels together, or stich panels together, use the blend, stack and mp4 commands.
Usage: dexp render [OPTIONS] INPUT_PATH
Options:
-o, --output_path TEXT Output folder to store rendered PNGs. Default is:
frames_<channel_name>
-c, --channels TEXT list of channels to render, all channels when
ommited.
-s, --slicing TEXT dataset slice (TZYX), e.g. [0:5] (first five
stacks) [:,0:100] (cropping in z).
-w, --overwrite to force overwrite of target [default: False]
-a, --aspect FLOAT sets aspect ratio e.g. 4 [default: 4]
-cm, --colormap TEXT sets colormap, e.g. viridis, gray, magma, plasma,
inferno [default: magma]
-rs, --rendersize INTEGER Sets the frame render size. i.e. -ws 400 sets the
window to 400x400 [default: 2048]
-cl, --clim TEXT Sets the contrast limits, i.e. -cl 0,1000 sets
the contrast limits to [0,1000]
-opt, --options TEXT Render options, e.g: 'gamma=1.2,box=True'.
Important: no white spaces!!! Complete list with
defaults will be displayed on first run
--help Show this message and exit.
Video compositing:
Takes frames and blend them together. Typically used for merging channels, but can also be used to add text -- if you provide a folder with a single PNG image of correct dimensions
Usage: dexp blend [OPTIONS] [INPUT_PATHS]...
Options:
-o, --output_path TEXT Output folder for blended frames.
-b, --blending TEXT Blending mode: max, add, addclip, adderf (add stands
for addclip). [default: max]
-w, --overwrite to force overwrite of target [default: False]
-k, --workers INTEGER Number of worker threads to spawn, set to -1 for
maximum number of workers [default: -1]
--help Show this message and exit.
Video stacking:
In addition to blending frames you can also stack frames horyzontally or vertically to make multi-panel videos. Again, here we just manipulate folders of PNG files.
Usage: dexp stack [OPTIONS] [INPUT_PATHS]...
Options:
-o, --output_path TEXT Output folder for blended frames.
-r, --orientation TEXT Stitching mode: horiz, vert [default: horiz]
-w, --overwrite to force overwrite of target [default: False]
-k, --workers INTEGER Number of worker threads to spawn, set to -1 for
maximum number of workers [default: -1]
--help Show this message and exit.
Conversion from frame sequences to mp4 file:
Takes a folder of PNG files and makes it into a MP4 file.
Usage: dexp mp4 [OPTIONS] INPUT_PATH
Options:
-o, --output_path TEXT Output file path for movie
-fps, --framerate INTEGER Sets the framerate in frames per second
[default: 30]
-w, --overwrite to force overwrite of target [default: False]
--help Show this message and exit.
Examples:
The folowing examples can be tested on existing datasets:
Gathers info on the dataset '2019-07-03-16-23-15-65-f2va.mch7' with napari:
dexp info 2019-07-03-16-23-15-65-f2va.mch7
Copies a z-max-projection for the first 10n timepoints (-s [0:10]) from scope acquisition '2019-07-03-16-23-15-65-f2va.mch7' to Zarr folder '~/Downloads/local.zarr', and overwrites whatever is there (-w).
dexp copy -w -p 1 -s '[0:10]' 2019-07-03-16-23-15-65-f2va.mch7 -o ~/Downloads/local.zarr
Views the first 100 times points '2019-07-03-16-23-15-65-f2va.mch7' with napari:
dexp view -s '[0:100]' 2019-07-03-16-23-15-65-f2va.mch7
Technical notes:
- You can pass arguments in any order for bash but not for all shells, i.e. zsh.
- You can pass string arguments as non string in bash but not in all shells.
Pro Tips
redirect to file and to standard output:
You can send the output to a log file and still be able to see the output by using the following postfix:
2>&1 | tee logfile.txt
Example:
dexp ... dexp parameters ... 2>&1 | tee logfile.txt
use tmux to keep track of long runing jobs
Why tmux? When you connect via network adn SSH, you can start a process on a remote machine, but it often occurs that closing the terminal or loosing the network connection will kill the running process. Even if one figures out how to keep the processs running, you rarely can see again the log outputs - unless you have explictely redirected to a file. tmux greatly simplifies all this by providing persistent terminal sessions.
First make sure that tmux is instaled on your system:
sudo apt-get install tmux
Connect to your machine using, for example, ssh:
ssh username@machine
Create the session in which you want to run your long-running process:
tmux new -s dexp
Once in your session you can activate the dexp environment, and start dexp, etc...
Important: You can leave a session by pressing the keys: CTRL+B then D
To come back to a session, you reattach:
tmux attach -t dexp
Once a session is created, it will remain active until you close it, no need to create it again (unless you have closed it!). You can disconnect your SSH session, loose network connection, close your computer, and still be able to reconnect to your session and have everything as if you had kept everything open.
In doubt, you can list all active sessions:
tmux ls
To close a session: First kill, if needed, the running process within the session by pressing CTRL+C or/and CTRL+Z, and then, simply type the command exit in the termnal within the session.
Note: you might encounter problems in tmux with text coloring. A solution is to change the default xterm setting:
First, generate a default configuration file for tmux:
tmux show -g | cat > ~/.tmux.conf
Add the following line at the end of that file (~/.tmux.conf):
set -g default-terminal "screen-256color"
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