Cyz2Json - Convert flow cytometry CYZ files to JSON format.

Introduction

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.

Build instructions

Build on the PC

Installation

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".

Build with GitHub actions

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.

On MacOSX

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.

Running the program

Options

The program has a set of arguments and options that can be passed to fit the kind of data you need :

• input the cyz file to be converted, mandatory,
• --output the JSON output file,
• --raw to not apply the moving weighted average filtering algorithm to pulse shapes, export raw, unsmoothed data,
• -V display version information,
• --metadatagreedy save all possible measurement settings with your file, default = true,
• --imaging-set-information to export set information for imaging,
• --imaging-set-definition to override the definitions stored in the file, only if --imaging-set-information is true for file with set definitions,
• --image-processing to 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-threshold the minimum pixel value difference from the background to be considered an object, default = 9,
• --image-processing-erosion-dilation the size of the erosion/dilation filter to apply after thresholding, default = 1,
• --image-processing-bright-field-correction correct the image for variation in the lighting, default = true,
• --image-processing-margin-base add a marging of this many pixels around the detected object, default = 25,
• --image-processing-margin-percentage add an extra margin that is a percentage of the size of the detected object, default = 10,
• --image-processing-extend-object-detection when seperate objects are detected close (in the margin) of the main object then extend the rectangle to include these objects as well, default = true.

Linux

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

On Windows

Cyz2Json.EXE input.cyz --output output.json

On MacOSX

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

Bulk file conversion

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

Processing CYZ JSON files

Using Python

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.

R example

To load a JSON flow cytometry data file into R:

library(jsonlite)

json_data <- fromJSON("pond.json")
print(json_data)

Notes

On images

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).

On the API

Cyz2json is using a dll from the CyzFile-API, at this moment, using version 1.6.1.0.

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 net8.0 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.

Acknowledgements

My thanks to the following organisations for supporting this work:

The Alan Turing Institute.

The Finnish Marine Research Infrastructure consortium (FINMARI)

The Centre for Environment, Fisheries and Aquaculture Science (Cefas)

CytoBuoy b.v.

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.

Disclaimers

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.