bio formats matlab

Loading...

Page contents

• Save as animated gif
• Bio‑Formats
• FIBSEM importer
• LSM Toolbox
• OlympusImageJPlugin
• Extract Images From PDF...
• TIA .ser folder export
• Vaa3d Reader
• Vaa3d Writer
• Wavefront .OBJ ...

Import data from many life sciences file formats, and export to several open formats.

See LOCI’s Bio-Formats site for a historical narrative of the project.

Documentation

What follows is a brief overview of the available plugins. You will find them all under the “Bio-Formats” submenu of Plugins. See the Bio-Formats website for additional information about Bio-Formats in general.

See especially the Using Bio-Formats page for detailed instructions.

Bio-Formats Importer

The Bio-Formats Importer is a plugin for reading data into Fiji. It can open many dozens of proprietary life sciences formats, and standardize their acquisition metadata into a common OME data model . It will also extract and set basic metadata values such as spatial calibration if they are available in the file.

Often, you will not need to worry about this plugin to import your data, because Bio-Formats is largely integrated with the File › Open command of Fiji. However, for certain file formats, you may wish to explicitly activate the Bio-Formats Importer to override the default behavior of Fiji. For example, by default Fiji uses some built-in logic to open TIFF files, but this logic may fail with certain TIFFs. The Bio-Formats Importer plugin may be able to import such TIFFs successfully.

Bio-Formats Exporter

The Bio-Formats Exporter is a plugin for exporting data to disk.

It can save to the open OME-TIFF file format, as well as several movie formats (e.g., QuickTime, AVI) and graphics formats (e.g., PNG, JPEG).

• Animated PNG (*.png)
• Audio Video Interleave (*.avi)
• CellH5 File Format (*.ch5)
• Encausupated PostScript (*.eps, *.epsi)
• Image Cytometry Standard (*.ids, *.ics)
• Java source code (*.java)
• JPEG (*.jpg, *.jpeg, *.jpe)
• JPEG-2000 (*.jp2)
• OME-TIFF (*.ome.tif, *.ome.tiff, *.ome.tf2, *.ome.tf8, *.ome.btf)
• OME-XML (*.ome, *.ome.xml)
• QuickTime (*.mov)
• Tagged Image File Format (TIFF) (*.tif, *.tiff, *.tf2, *.tf8, *.btf)
• Vaa3d (*.v3draw)
• Woolz (*.wlz)

For OME-TIFF and TIFF formats, the file extensions *.tif and *.tiff are associated with the standard 32-bit TIFF, which has a 4GB size limit. On the other hand, the file extensions *.tf2 , *.tf8 , and *.btf are automatically associated with the 64-bit BigTIFF format , which can store much bigger data.

Bio-Formats Remote Importer

The Bio-Formats Remote Importer is a plugin for importing data from a remote URL.

It is likely to be less robust than working with files on disk, so when possible we recommend downloading your data to disk and using the regular Bio-Formats Importer instead.

Bio-Formats Windowless Importer

The Bio-Formats Windowless Importer is a version of the Bio-Formats Importer plugin that runs with the last used settings to avoid popping up any additional dialogs beyond the file chooser. If you find that you always use the same import settings, you may wish to use the windowless importer to save time.

Bio-Formats Macro Extensions

The Bio-Formats plugins come with a set of macro extensions to enable additional functionality from macros. The Bio-Formats Macro Extensions plugin prints out the available commands to the ImageJ log window, along with instructions for using them.

Stack Slicer

The Stack Slicer plugin is a helper plugin used by the Bio-Formats Importer . It can also be used standalone to split a stack across channels, focal planes or time points.

Bio-Formats Plugins Configuration

The Bio-Formats Plugins Configuration dialog is a useful way to configure the behavior of each file format. You can see a list of supported file formats on the Formats tab, toggle each format on or off (which is useful, for example, if your file is being detected as the wrong format), and toggle whether each format bypasses the importer options dialog using the “Windowless” checkbox. You can also configure any specific options for each format—for example, for QuickTime, you can toggle between Apple’s QTJava library or Bio-Formats’s built-in support.

In addition, you can see a list of available helper libraries used by Bio-Formats on the Libraries tab.

Bio-Formats Plugins Shortcut Window

The Bio-Formats Plugins Shortcut Window is a small window with a quick-launch button for each plugin. You can also drag and drop files onto the shortcut window to open them quickly using the Bio-Formats Importer plugin.

Update Bio-Formats Plugins

The Update Bio-Formats Plugins command will check online for updates to the Bio-Formats Plugins. In the case of Fiji, we recommend that you do not use this method of update, but instead use the ImageJ Updater .

Calling Bio-Formats from the command line

You can invoke Bio-Formats from the command line using the ImageJ Launcher :

• Use the Macro Recorder to record the line of macro code that runs Bio-Formats that way you want.
• Click “Create” to pop up the Script Editor , edit as desired, then save the macro as a .ijm macro file.
• Run the macro from the command line; e.g.:

Leave off the -batch flag if you want ImageJ to remain open afterward.

Note that you cannot use the –headless option because Bio-Formats does not work in headless mode, even when running as a macro. (You will see VerifyError on the console if you try.)

Here is an example macro created in such a fashion:

Bio-Formats has a high-level scripting interface, accessible by Java and all scripting languages supported by Fiji (but not the ImageJ macro language). Java example:

If needed, import options can be set:

Daily builds

The daily builds are not yet released and should be considered beta in quality. There may be new bugs. In particular, you should avoid exporting data using the Bio-Formats Exporter because the files it writes might not be readable later by release versions of Bio-Formats or other OME-compliant tools.

Fiji ships release versions of Bio-Formats. However, given the long time frame between releases, you can update to the latest code by toggling the Bio-Formats update site, which includes the latest bug-fixes.

When reporting a bug, the developers may ask you to test with the Bio-Formats update site enabled.

To enable the Bio-Formats update site:

• Launch the updater: Update from the Help menu.
• Click the Manage update sites button.

• Click the Apply changes button.
• Restart Fiji when prompted.

The Bio-Formats source code is on GitHub .

Reporting bugs

To report a bug in Bio-Formats, please see reporting a bug in Bio-Formats .

Publication

doi:10.1083/jcb.201004104

• Design: HTML5 UP

Home - Biofrontiers-ALMC/bioformats-matlab GitHub Wiki

Welcome to the Bioformats Image Toolbox wiki!

The Bioformats Image Toolbox provides a way to read microscope files (such as Nikon's ND2 format) into MATLAB. The toolbox implements a MATLAB class around the Open Microscopy Environment group's Bio-Formats Image Package Java library.

Example usage

Downloads and installation.

Please visit the Releases page to download the latest version. You only need the MATLAB toolbox ( .mltbx ) file, not the source code.

Documentation

• Getting started - Download, installation, and basic tasks
• Contents - List of all user documentation
• Index - List of all functions, classes, and terminology

Bug report and Feature Requests

Please submit bug reports or ideas for new features on the Issues Board .

For bug reports, please provide enough details to reproduce the error, including details of external files used. If possible, please include a minimal example that produces the error and post that. Please also include the full error message at the end of the report.

Known issues:

2020/04/13 - Working with ND2 files that have been cropped in Nikon Elements can result in odd problems such as images appearing out of order or timestamps being nonsensical.

Workaround: If you are using Windows or Linux, you can try using an alternative ND2 reader that uses the official SDKs

Contributer Guide

• Developer's Guide

License and acknowledging the project

We would appreciate an acknowledgement in your publications or presentations. An example acknowledgement statement is:

This project uses the MATLAB Bioformats Image Toolbox developed by Dr. Jian Wei Tay of the BioFrontiers Advanced Light Microscopy Core at the University of Colorado Boulder.

We also ask that you send us an email at [email protected] so we can keep track of usage stats. This helps us in reporting and securing funding for the facility.

This project is provided under the MIT License.

⚠️ **GitHub.com Fallback** ⚠️

• Accessibility

• Documentation

Bio-Formats

• Partner Projects
• OME Model and Formats
• Contributing to OME
• User Help Website
• Previous versions
• Mailing Lists
• News and Events
• Minutes and Meetings
• Script Sharing
• Report an Issue
• Job Openings with OME
• Use Our Logos
• The OME Teams
• Contributors
• Commercial Partners
• Publications
• Licensing & Attribution
• Bio-Formats 5.1.10 documentation »
• User Information »

Page Contents

• Installation
• Performance
• Alternative scripts

Previous topic

Quick search.

Enter search terms or a module, class or function name.

• Show Source
• Show on GitHub
• Edit on GitHub

MATLAB is a high-level language and interactive environment that facilitates rapid development of algorithms for performing computationally intensive tasks.

Calling Bio-Formats from MATLAB is fairly straightforward, since MATLAB has built-in interoperability with Java. We have created a set of scripts for reading image files. Note the minimum supported MATLAB version is R2007b (7.5).

Installation ¶

Download the MATLAB toolbox from the Bio-Formats downloads page . Unzip bfmatlab.zip and add the unzipped bfmatlab folder to your MATLAB path.

As of Bio-Formats 5.0.0, this zip now contains the bundled jar and you no longer need to download loci_tools.jar or the new bioformats_package.jar separately.

Please see Using Bio-Formats in MATLAB for usage instructions. If you intend to extend the existing .m files, please also see the developer page for more information on how to use Bio-Formats in general.

Performance ¶

In our tests (MATLAB R14 vs. java 1.6.0_20), the script executes at approximately half the speed of our showinf command line tool , due to overhead from copying arrays.

Upgrading ¶

To use a newer version of Bio-Formats, overwrite the content of the bfmatlab folder with the newer version of the toolbox and restart MATLAB.

Alternative scripts ¶

Several other groups have developed their own MATLAB scripts that use Bio-Formats, including the following:

• https://github.com/prakatmac/bf-tools/
• imread for multiple life science image file formats

Navigation Menu

Search code, repositories, users, issues, pull requests..., provide feedback.

We read every piece of feedback, and take your input very seriously.

Saved searches

Use saved searches to filter your results more quickly.

To see all available qualifiers, see our documentation .

• Notifications You must be signed in to change notification settings

A MATLAB class using the OME Bio-Formats library

Biofrontiers-ALMC/bioformats-matlab

Folders and files.

Repository files navigation

Bioformats image toolbox.

Welcome to the Bioformats Image Toolbox!

The Bioformats Image Toolbox provides a way to read microscope files (such as Nikon's ND2 format) into MATLAB. The toolbox implements a MATLAB class to use the Bio-Formats Image Package Java library.

Prerequisites

• MATLAB R2016b or newer (it is highly likely that an earlier version will work).

Quick Navigation

• Released toolboxes
• Documentation

This project uses the OME Bio-Formats Library .

Acknowledging us

We would appreciate an acknowledgement in your publications or presentations. An example acknowledgement statement is:

This project is developed by Dr. Jian Wei Tay of the BioFrontiers Advanced Light Microscopy Core at the University of Colorado Boulder.

We also ask that you send us an email at [email protected] so we can keep track of usage stats. This helps us in reporting and securing funding for the facility.

This project is provided under the MIT License.

• MATLAB 100.0%

• MATLAB Answers
• File Exchange
• AI Chat Playground
• Discussions
• Communities
• Treasure Hunt
• Community Advisors
• Virtual Badges
• MathWorks.com
• Trial software

You are now following this Submission

• You may receive emails, depending on your communication preferences

Bioformats Image Toolbox

• Open in MATLAB Online
• Version History
• Reviews (0)
• Discussions (0)

Welcome to the Bioformats Image Toolbox!

The Bioformats Image Toolbox provides a way to read microscope files (such as Nikon's ND2 format) into MATLAB. The toolbox implements a MATLAB class to use the Bio-Formats Image Package Java library.

Prerequisites

• MATLAB R2016b or newer (it is highly likely that an earlier version will work).

Quick Navigation

• Released toolboxes
• Documentation

This project uses the OME Bio-Formats Library .

Acknowledging us

We would appreciate an acknowledgement in your publications or presentations. An example acknowledgement statement is:

This project is developed by Dr. Jian Wei Tay of the BioFrontiers Advanced Light Microscopy Core at the University of Colorado Boulder.

We also ask that you send us an email at [email protected] so we can keep track of usage stats. This helps us in reporting and securing funding for the facility.

This project is provided under the MIT License.

JWTay (2024). Bioformats Image Toolbox (https://github.com/Biofrontiers-ALMC/bioformats-matlab/releases/tag/v1.2.3), GitHub. Retrieved July 5, 2024 .

MATLAB Release Compatibility

Platform compatibility, tags add tags, community treasure hunt.

Find the treasures in MATLAB Central and discover how the community can help you!

Discover Live Editor

Create scripts with code, output, and formatted text in a single executable document.

Learn About Live Editor

• BioformatsImage

Select a Web Site

Choose a web site to get translated content where available and see local events and offers. Based on your location, we recommend that you select: .

You can also select a web site from the following list

How to Get Best Site Performance

Select the China site (in Chinese or English) for best site performance. Other MathWorks country sites are not optimized for visits from your location.

• América Latina (Español)
• Canada (English)
• United States (English)
• Belgium (English)
• Denmark (English)
• Deutschland (Deutsch)
• España (Español)
• Finland (English)
• France (Français)
• Ireland (English)
• Italia (Italiano)
• Luxembourg (English)
• Netherlands (English)
• Norway (English)
• Österreich (Deutsch)
• Portugal (English)
• Sweden (English)
• United Kingdom (English)

Asia Pacific

• Australia (English)
• India (English)
• New Zealand (English)
• 简体中文 Chinese
• 日本 Japanese (日本語)
• 한국 Korean (한국어)

Contact your local office

Bioinformatics Toolbox

Read, analyze, and visualize genomic and proteomic data.

Have questions? Contact Sales .

Bioinformatics Toolbox provides algorithms and apps for building bioinformatics pipelines, Next Generation Sequencing (NGS), microarray analysis, mass spectrometry, and gene ontology. You can read genomic and proteomic data and explore this data with the Genomics Viewer app and visualize with spatial heatmaps and clustergrams. The toolbox (with Statistics and Machine Learning Toolbox) provides statistical, regression, classification, and (with Deep Learning Toolbox) deep learning techniques to build complete analysis pipelines.

The Biopipeline Designer app lets you interactively build bioinformatics pipelines for genomic data analysis, locally or in the cloud. You can use a combination of built-in bioinformatics pipeline blocks that integrate proven NGS libraries and custom blocks to extend analyses with community tools. You can create a pipeline to preprocess reads, map them to a reference genome, and perform statistical analysis, like RNA-Seq differential expression analysis or ChIP-Seq analysis.

Build Bioinformatics Pipelines

With the Biopipeline Designer app you can interactively build and run end-to-end bioinformatics pipelines, locally or in the cloud. Build a pipeline with built-in blocks that integrate proven NGS libraries or custom blocks to extend analyses with community tools for each step in the process. Run pipelines in parallel (using Parallel Computing Toolbox) and in batch mode.

Documentation  |  Examples

Next Generation Sequencing (NGS)

The toolbox provides algorithms and visualization techniques for NGS. For example, you can preprocess reads, map them to a reference genome, and perform statistical analyses, such as differential expression analysis from RNA-Seq data or ChIP-Seq data analysis.

Documentation | Examples

Sequence Analysis

Apply sequence analysis methods, including pairwise sequence, sequence profile, and multiple sequence alignment. Manipulate and evaluate sequences to gain a deeper understanding of your data. Perform BLAST searches against known sequences in online or local databases.

Documentation | Example

Mass Spectrometry Data Analysis

Bioinformatics Toolbox enables the analysis of SELDI, MALDI, LC/MS, and GC/MS data. You can smooth, align, and normalize spectra and use classification, statistical, and machine learning techniques to create classifiers and identify potential biomarkers.

Phylogenetic Tree Analysis

Construct phylogenetic trees using hierarchical linkage with a variety of techniques, including neighbor joining, single and complete linkage, and Unweighted Pair Group Method Average (UPGMA).

Reading Genomic and Proteomic Data

You can read data from common file formats such as SAM, BAM, FASTA, FASTQ, GTF, and GFF and from online databases such as NCBI Gene Expression Omnibus, GenBank ® , and the Sequence Read Archive. You can use specialized data containers for data too large to fit in memory.

Statistical and Machine Learning Algorithms

Bioinformatics Toolbox provides functions that build on the Statistics and Machine Learning Toolbox , which offers interactive tools for feature selection, classification, regression, mapping, and displaying hierarchy plots and pathways.

Microarray Data Analysis

­Normalize microarray data using a variety of methods. Identify differentially expressed genes and perform enrichment analysis of expression results using gene ontology. Visualize gene and protein-protein interaction networks using graph theory algorithms.

Deploying and Sharing Apps

Turn your data analysis program into a customized software application. Build custom user interfaces; integrate with existing C, C++, and Java™ applications; and deploy standalone apps.

Product Resources:

"MATLAB enables young biologists to learn enough programming and math without being afraid of the code. They can write in MATLAB as if it were English." Dr. Jonas Almeida, Medical University of South Carolina

Get a Free Trial

30 days of exploration at your fingertips.

Ready to Buy?

Get pricing information and explore related products.

Are You a Student?

Your school may already provide access to MATLAB, Simulink, and add-on products through a campus-wide license.

What's Next?

CUSTOMER STORY

Centers for Disease Control and Prevention Automates Poliovirus Sequencing and Tracking

Sequence viewer app.

SUPPORT PACKAGE

Bioinformatics Toolbox Software Support Packages

Select a Web Site

Choose a web site to get translated content where available and see local events and offers. Based on your location, we recommend that you select: .

You can also select a web site from the following list

How to Get Best Site Performance

Select the China site (in Chinese or English) for best site performance. Other MathWorks country sites are not optimized for visits from your location.

• América Latina (Español)
• Canada (English)
• United States (English)
• Belgium (English)
• Denmark (English)
• Deutschland (Deutsch)
• España (Español)
• Finland (English)
• France (Français)
• Ireland (English)
• Italia (Italiano)
• Luxembourg (English)
• Netherlands (English)
• Norway (English)
• Österreich (Deutsch)
• Portugal (English)
• Sweden (English)
• United Kingdom (English)

Asia Pacific

• Australia (English)
• India (English)
• New Zealand (English)
• 简体中文 Chinese
• 日本 Japanese (日本語)
• 한국 Korean (한국어)

Contact your local office

Matlab Toolbox not containing latest version of bioformats_package.jar?

I downloaded the Matlab Toolbox from Bio-Formats Downloads (OME) , but when I ran bfUpgradeCheck I receive the following:

A new stable version of Bio-Formats is available

version = char(loci.formats.FormatTools.VERSION);

Returns version=5.1.2 rather than the expected 6.6.1 or equivalent.

Should Matlab’s jar be behind the current release? And if not, can the 6.6.1 Bio-Formats Package be switched out in the Matlab files?

I checked the newly-downloaded version because I was receiving a “Java Exception Error: Missing Library Java Advanced Imaging (JAI)”.

I tried to switch out bioformas_package.jar(6.6.1) and then received:

log4j:WARN No appenders could be found for logger (loci.formats.ClassList). log4j:WARN Please initialize the log4j system properly. ERROR: Java exception occurred: loci.formats.FormatException: No IFDs found

I am running MATLAB 2021a and have Java 8 SE. Any help greatly appreciated.

Hi @KE06 , I double checked the latest version of the toolbox and the jar it contains is the correct 6.6.1 version. What looks to be happening is a conflict with a previous version which has been installed. If you run the command javaclasspath do you see any other versions of bioformas_package in a different location?

Hi @dgault my dynamic path returns a single instance of bioformats_package.jar in my current working folder. Static path returns the expected series.

As reference: I downloaded the Matlab Toolbox from the website, deleted my prior bioformats folder, and pasted in the freshly downloaded folder.

Within Matlab if you go to your current working folder, expand the bioformats_package.jar and look for the file META-INF/MANIFEST.MF and open it, you should see details as below. Does your jar show the version as 6.6.1 here?

Thanks @dgault for your previous assistance! From your help and for future readers, I was able to determine that running my prior code was calling a previous instance of Bioformats elsewhere within my computer (v 5.1.2) regardless of having v6.6.1 packaged in the same folder as my Matlab script. I admit to not knowing why this happened (or specifically where in the computer it was being called from) but changing the computer path of the image I was calling resolved:

Java Exception Error: Missing Library Java Advanced Imaging (JAI)

Furthermore,

Turned out to be the original image file was also corrupted and could not be viewed by our Whole Slide Image viewer independent of Bioformats.

Related Topics

• Stack Overflow for Teams Where developers & technologists share private knowledge with coworkers
• Advertising & Talent Reach devs & technologists worldwide about your product, service or employer brand
• OverflowAI GenAI features for Teams
• OverflowAPI Train & fine-tune LLMs
• Labs The future of collective knowledge sharing
• About the company Visit the blog

Collectives™ on Stack Overflow

Find centralized, trusted content and collaborate around the technologies you use most.

Q&A for work

Connect and share knowledge within a single location that is structured and easy to search.

Get early access and see previews of new features.

BioFormats In Matlab

I am attempting to implement bio-formats into matlab to run with matlab code the process nd2 microscopy images and quantify them. I am trying to within Matlab directly convert files from nd2>tiff format. If anyone has any guidance as to how I can do this, Please let me know. I have tried using the bfconvert function and it doesn't seem to work. I have also downloaded bftools.zip and bfmatlab.zip.I am wondering if I have to do an integration to allow matlab code to properly function with Java language.

• image-processing
• file-conversion

• MATLAB works fine with Java as it is implemented in BioFormats. There shouldn't be any need to make extra declarations or integrations as long as the .jar file is in the proper location on your machine. Can you provide an example of your code and the error that is generated? –  Staus Commented Nov 4, 2014 at 23:42
• Hello Thanks so much for your response. I am new to MATLAB and programming so all of this is confusing me. I basically can not figure out how to convert from nd2>tiff within Bioformats. I know there is code I am suppose to write to be able to do this but I can't figure it out. Please help! –  Sibley Bardales Commented Nov 5, 2014 at 1:06
• openmicroscopy.org/site/support/bio-formats5/developers/… –  Sibley Bardales Commented Nov 5, 2014 at 1:07
• I have been using this.. –  Sibley Bardales Commented Nov 5, 2014 at 1:08
• There is a function called bfconvert that is part of the bftools package but it is not a MATLAB file. It is a command-line interface that you call from the command prompt on your machine. This can be called through MATLAB if it has to be, but that is a pretty roundabout way of doing it. According to the documentation it will directly convert your ND2 files into TIFFs and should be pretty fast. If you need to do this in MATLAB (or you want to manipulate the data before saving it as a TIFF) then you can use the bfopen and bfsave tools in the bfmatlab toolbox. –  Staus Commented Nov 5, 2014 at 2:11

Know someone who can answer? Share a link to this question via email , Twitter , or Facebook .

Your answer.

Reminder: Answers generated by artificial intelligence tools are not allowed on Stack Overflow. Learn more

Sign up or log in

Post as a guest.

Required, but never shown

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy .

Browse other questions tagged image matlab image-processing file-conversion or ask your own question .

• The Overflow Blog
• Community Products Roadmap Update, July 2024
• Featured on Meta
• We spent a sprint addressing your requests — here’s how it went
• Upcoming initiatives on Stack Overflow and across the Stack Exchange network...
• Policy: Generative AI (e.g., ChatGPT) is banned
• The [lib] tag is being burninated
• What makes a homepage useful for logged-in users

Hot Network Questions

• Do you always experience the gravitational influence of other mass as you see them in your frame?
• What is the "closest approximation" to fields by an equational variety?
• Understanding Polynomial Rolling Hash Function by Modular Arithmetic
• Can I improve my code to extract permutation cycles from a (n,2) matrix?
• Optimizing Pi Estimation Code
• Why does `p` not put all yanked lines after quitting and reopening Vim?
• What is the reason for using decibels to measure sound?
• Why does independent research from people without formal academic qualifications generally turn out to be a complete waste of time?
• Gradual light transition
• Does Justice Sotomayor's "Seal Team 6" example, in and of itself, explicitly give the President the authority to execute opponents? If not, why not?
• Don't make noise. OR Don't make a noise
• error when re-applying the permissions script into the original database - sql server
• Can you be charged with breaking and entering if the door was open, and the owner of the property is deceased?
• confidence intervals for proportions containing a theoretically impossible value (zero)
• Can a country refuse to deliver a person accused of attempted murder?
• What determines the orders of flats or sharps appearing on a key signature? why is it not just top to bottom?
• Can player build dungeons in D&D? I thought that was just a job for the DM
• When do people say "Toiletten" in the plural?
• Family reunion crossword: The case of the missing letters
• Why did the main wire to my apartment burn before the breaker?
• Cliffhanger ending?
• Food for thought: Which person has truth in this discussion on capacity and AC?
• Strange Interaction with Professor
• When selling a machine with proprietary software that links against an LGPLv3 library, do I need to give the customer root access?