This program converts flow cytometry data stored in a CytoBuoy CYZ format file to JSON format.
Although CYZ files work with the Cytobuoy supplied CytoClus program, we want to access the data from a wider set of data science tooling including Python and R. We therefore convert to JSON.
This program uses the CytoBuoy CyzFile API and targets the Microsoft .NET 8 framework on Windows, macOS or Linux.
The first step is to install the Microsoft dotnet runtime version 8. Microsoft provides detailed instructions at https://learn.microsoft.com/en-us/dotnet/core/install/.
For example, installation on Linux Ubuntu 22.04 is as follows:
sudo apt-get update && sudo apt-get install -y dotnet-sdk-8.0
You can test that dotnet is installed on your system by typing:
dotnet --info
To generate the version number, you will need to install the nbgv tool.
You can install this tool by typing:
dotnet tool install -g nbgv
The Cyz2Json program can then be compiled by cloning the project from GitHub and typing dotnet build -p:OutputPath=./bin/.
The default version is the one given by the Cyz2Json.csproj file (unless passed directly during build via -p:Version), the assembly informal version is "Cyz2Json-the current Version-the latest Git SHA".
The Release-Cyz2Json.yml workflow can be triggered manually to build and publish a release of the tool with cross platform binaries. A tag is required to be used as the release and tool version (replacing the default one), and a reason for the release can be given as well though it is not mandatory.
You will find the result in : https://github.com/OBAMANEXT/cyz2json/actions and release in : https://github.com/OBAMANEXT/cyz2json/releases
To install from release, download the release for you platfrom, and unpack on your folder choice.
You will need to bypass security You have 2 possibilities : using xattr command. for exmaple:
xattr -d com.apple.quarantine /opt/cytosense_to_ecotaxa_pipeline/bin/*
or if you do not want to use xattr you need to go in Systems Settings > Security & Privacy > General and allow the app to be opened for the 10+ libraries. You need to relauch sevaral time the cyz2json binary to acheive all neccessary permissions.
The program has a set of arguments and options that can be passed to fit the kind of data you need :
inputthe cyz file to be converted, mandatory,--outputthe JSON output file,--rawto not apply the moving weighted average filtering algorithm to pulse shapes, export raw, unsmoothed data,-Vdisplay version information,--metadatagreedysave all possible measurement settings with your file, default = true,--imaging-set-informationto export set information for imaging,--imaging-set-definitionto override the definitions stored in the file, only if --imaging-set-information is true for file with set definitions,--image-processingto perform cropping and image processing during the export of the image, default = false, this comes along with several other arguments to adjust the processing options :--image-processing-thresholdthe minimum pixel value difference from the background to be considered an object, default = 9,--image-processing-erosion-dilationthe size of the erosion/dilation filter to apply after thresholding, default = 1,--image-processing-bright-field-correctioncorrect the image for variation in the lighting, default = true,--image-processing-margin-baseadd a marging of this many pixels around the detected object, default = 25,--image-processing-margin-percentageadd an extra margin that is a percentage of the size of the detected object, default = 10,--image-processing-extend-object-detectionwhen seperate objects are detected close (in the margin) of the main object then extend the rectangle to include these objects as well, default = true.
The program can be run, on Linux, for example, as follows:
dotnet bin/Cyz2Json.dll input.cyz --output output.json
Running with executable loaded from github
export cyzversion=v0.0.49
rm -rf cyz2json/* && curl -L -o cyz2json/cyz2json.zip https://github.com/ecotaxa/cyz2json/releases/download/$cyzversion/cyz2json-ubuntu-latest.zip && pushd cyz2json && unzip cyz2json.zip && popd && export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:. && cyz2json/Cyz2Json ./Deployment\ 1\ 2024-07-18\ 21h12.cyz --metadatagreedy=false --output ./Deployment\ 1\ 2024-07-18\ 21h12.json
Cyz2Json.EXE input.cyz --output output.json
bypass security with xattr command
xattr -d com.apple.quarantine ./cyz2json-macos-latest/*
2 methods to run
dotnet bin/Cyz2Json.dll input.cyz --output output.json
or
Cyz2Json.exe input.cyz --output output.json
We often find ourselves needing to undertake a bulk conversion of a large set of files. The following shell script can help:
#!/usr/bin/env bash
for file in *.cyz
do
dotnet ~/git/Cyz2Json/bin/Cyz2Json.dll "$file" --output "$file".json
done
You may run into the System.DllNotFoundException: Unable to load shared library 'OpenCvSharpExtern' or one of its dependencies. when trying to run the program. In that case, either the library OpenCvSharpExtern and/or its dependencies are missing or the path to load them is wrong. Here are a few steps to help you deal with this problem if you ever run into it.
The libOpenCvSharpExtern.so library should be exported by the OpenCvSharp4.official.runtime.linux-x64 nugget package and found either in the latest release asset or in your local build results. It is statically linked to its dependencies which are not themselves exported. Most of those libraries are pre-installed in standard ubuntu distributions, but can be missing in minimal environment/containers. Besides, if you are using the latest release asset, the version of the dependencies you have locally might not be compatible with the versions linked to the library exported in the asset (should be latest "dev" versions).
To fix this, the easiest way is to :
- move to your binaries folder (either the downloaded asset or the result of the local build) and run the
ldd libOpenCvSharpExtern.socommand, this will list all statically linked dependencies and highlight missing ones as "not found", - then update and/or install those libraries.
Example of installation :
sudo apt-get update
sudo apt-get install -y \
libgtk-3-dev \
libtesseract-dev \
libavcodec-dev \
libavformat-dev \
libavutil-dev \
libswscale-dev \
libopenexr-dev \
libtiff-dev
The libOpenCvSharpExtern.dylib library should be exported with its dependencies either by the OpenCvSharp4.runtime.osx.10.15-x64 or the OpenCvSharp4.runtime.osx_arm64 nugget packages. A known issue with the macOS (arm64) version of the library is its hard dependency on the @executable_path/../dirs path, basically, it looks for native dependencies in this folder, that doesn't exist, instead of the folder where they are actually exported (the same as the libOpenCvSharpExtern.dylib file). You can check that by running the command otool -L libOpenCvSharpExtern.dylib and see the list of all dependencies and where the program will search them.
The easiest way to deal with this issue is by using an environment variable (via a shell script) :
#!/usr/bin/env bash
dll_path="bin/Cyz2Json.dll"
export DYLD_FALLBACK_LIBRARY_PATH=$(dirname $dll_path)
dotnet $dll_path input.cyz --output output.json
This will tell the program to try the path given by DYLD_FALLBACK_LIBRARY_PATH if all other (wrong) paths fail. In the example above, the native libraries are located in the same folder as the Cyz2Json.dll (dll_path), if it is not the case for you (for example they are in runtimes/osx-arm64/native/ folder) then simply modify the script to match your local directory structure.
Another issue is that the program is looking for an OpenCvSharpExtern.dylib file instead of the correct libOpenCvSharpExtern.dylib. The easiest way to correct this error is by creating a symlink : ln -sf libOpenCvSharpExtern.dylib OpenCvSharpExtern.dylib so any call to OpenCvSharpExtern.dylib will redirect to libOpenCvSharpExtern.dylib. The symlink was already created for the latest release asset and should be preserved.
You may run into the following error on Linux when trying to execute the program :
GC heap initialization failed with error 0x8007000E
Failed to create CoreCLR, HRESULT: 0x8007000E`
This problem is machine specific, check with the command ulimit -a that your virtual memory and max memory size are set either to unlimited or a large enough number. You can also check cat /proc/sys/vm/overcommit_memory, the value should be 0 (overcommit reasonable memory request on the heuristics base, default) or 1 (always overcommit). If it is set to 2 then it means never overcommit.
To bypass those problems, you can :
- temporarily set the virtual memory to unlimited
ulimit -v unlimited, - or temporarily change the overcommit mode to 1 (or 0)
echo 1 | sudo tee /proc/sys/vm/overcommit_memory, - you can also set an environment variable to temporarily lower the memory usage of the program (but be mindful of the value used if it is too small) :
export DOTNET_GCHeapHardLimit=1C0000000.
To load a JSON flow cytometry data file into Python:
import json
data = json.load(open("pond.json", encoding="utf-8-sig"))
print(data)
Note the need to explicitly specify the encoding to deal with Microsoft's and Python's differences in interpretation of the standards regarding byte order marks in UTF-8 files.
To load a JSON flow cytometry data file into R:
library(jsonlite)
json_data <- fromJSON("pond.json")
print(json_data)
If a CYZ file contains images, we currently base64 encode them and include them inline in the JSON. This is costly in terms of disk and only time will tell if it is a sensible design decision. A future enhancement would be to include a flag that writes the files out as JPEG images.
Note that the images are un-cropped by default. The --image-processing option can now be used to process and crop images when exporting.
Initially, the tool didn't support cropping as an expedience to allow cross platform operation (The CyzFile-API only supports cropping on Windows platforms).
Cyz2json is using a dll from the CyzFile-API.
To update you can use the API-update-from-tags.yml workflow which fetches the latest version of the API (in tags), you can run it manually or let it work on schedule (15th of each month), in that case, it compares the latest tag with the current version in this repo to choose whether to update or not.
You can also update manually without the workflow, to do so :
- download the latest release from https://github.com/Cytobuoy/CyzFile-API/releases,
- unzip the downloaded file,
- copy the files from the dll folder to the CyzFile folder,
- rebuild the project.
My thanks to the following organisations for supporting this work:
The Finnish Marine Research Infrastructure consortium (FINMARI)
The Centre for Environment, Fisheries and Aquaculture Science (Cefas)
I am grateful to Rob Lievaart at Cytobuoy for providing the libraries, code and examples on which this software is based. The CyzFile-API is licensed under the terms described in CyzFile-API_LICENSE.TXT.
Thanks to Eric Payne at Cefas for Visual Studio wizardry.
The OBAMA-NEXT project has been approved under HORIZON-CL6-2022-BIODIV-01-01: Observing and mapping biodiversity and ecosystems, with particular focus on coastal and marine ecosystems (Grant Agreement 101081642). Funded by the European Union and UK Research and Innovation. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or UK Research and Innovation. Neither the European Union nor the granting authority can be held responsible for them.