Skip to content
  • Home
  • Resources
  • Support
  • Contributors
  • Get Involved
  • About
Search
Login
Create Account

0
FAQ
→
Forum
0
Posts
-
Javadoc
Filter by type
Plugin Script Protocol FAQ Forum Topic Article
Filter by category
3-D3D3D coordinatesalignmentbasicsbatch processingCalciumcell trackingCLEMcolocalizationcomptageconfocalconnected componentscontributionconvolutioncorrelationdeconvolutiondeformable registrationdenoisingdetectiondetectordeveloperdisplacementsdistance mapexportezplugfeature detectionfeature matchingfilteringfluorescenceguiheadlesshelperHSV visualisationimage processImageJintensitymaskmavenmeasurementMHTmicroscopymonitoringmorphologymultiple hypothesis trackingnon rigid registrationoperatoroptimizationotsupluginpoint-spread functionprojectionprotocolPSFpythonregistrationreleaseRipley's K functionroiscriptscriptingsegmentationsequencesmoothingspatial distributionspotspot countstatisticssurfacesyntheticthresholdtoolboxtoolstrack processortrackingtutorialwarpingwavelet transformwaveletswidefieldworkbookXLS output
  • Plugin Script Protocol FAQ Forum Topic Article
  • 3-D
  • 3D
  • 3D coordinates
  • alignment
  • basics
  • batch processing
  • Calcium
  • cell tracking
  • CLEM
  • colocalization
  • comptage
  • confocal
  • connected components
  • contribution
  • convolution
  • correlation
  • deconvolution
  • deformable registration
  • denoising
  • detection
  • detector
  • developer
  • displacements
  • distance map
  • export
  • ezplug
  • feature detection
  • feature matching
  • filtering
  • fluorescence
  • gui
  • headless
  • helper
  • HSV visualisation
  • image process
  • ImageJ
  • intensity
  • mask
  • maven
  • measurement
  • MHT
  • microscopy
  • monitoring
  • morphology
  • multiple hypothesis tracking
  • non rigid registration
  • operator
  • optimization
  • otsu
  • plugin
  • point-spread function
  • projection
  • protocol
  • PSF
  • python
  • registration
  • release
  • Ripley's K function
  • roi
  • script
  • scripting
  • segmentation
  • sequence
  • smoothing
  • spatial distribution
  • spot
  • spot count
  • statistics
  • surface
  • synthetic
  • threshold
  • toolbox
  • tools
  • track processor
  • tracking
  • tutorial
  • warping
  • wavelet transform
  • wavelets
  • widefield
  • workbook
  • XLS output
Icy cheat sheets
Migrate your old Icy plugin to maven

How to get help on the Icy software?

In this article, we explain how to get help regarding the Icy software, an Icy plugin or protocol, and more generally bioimage analysis with Icy.

Read the documentation

It may seem obvious, but the first thing to do is to look into the documentation.

The Icy download page and the FAQ contain general information regarding installation of Icy, memory usage, publication of protocols or plugins.

Then, there is one documentation page per plugin on the Icy website. Search the plugin name in the search bar of the Icy software, and right click on its name to open the online documentation.

Online documentation on the Icy website is accessible via the search bar of the Icy software. Right click on the name of a plugin to access its documentation.

You can also search directly from the website. This can be useful when you are looking for more general information, for instance, you could type “segmentation” to search for plugins which can do segmentation in Icy.

For scripts and protocols creation, we recommend looking at examples of scripts and examples of protocols to get inspired. You can use the search bar on these pages to search only through scripts or protocols.

For plugin developement, you can also search through the Icy javadoc and/or get inspiration by looking at the Icy plugins from the Bioimage Analysis unit that are publicly available on the GitLab server of the Pasteur Institute.

We also gather training materials on the Icy training page. You will find slides, documents and links to online webinars.

Last but not least, all questions asked on the image.sc forum constitute an extra source of information. You can search the forum with keywords and/or with the tag icy.

Troubleshoot the issue

Often, experimenting a bit around a problem can help solve it. As for any kind of scientific experiment, write carefully everything you try. If you ask someone else for help later, this person will be happy to 1. see that you tried by yourself and 2. not have to go through this troubleshooting.

The plugin you use is displaying an error message

Read the error message. Often, the message will be unclear to you because it refers to some Java code of the plugin, but it sometimes contains readable information relative to a specific part of the plugin.

Experiment with the plugin to reproduce the error and answer the following questions:

  • What is the sequence of events leading to this error message? In other words, where did you click and in which order? Did you open an image?
  • Does it happens all the times or only sometimes? When does it happen, when not?
  • Does it happens whatever the type of image (2D, 3D, 3D+time) you use or whatever the type of ROIs?

The protocol you are creating/working with is giving you an error message or producing a different output than what you expect.

If there is an error message, read it. Identify the block(s) that are causing the problem. This block usually displays a white cross over a red disk in its upper right corner as a warning sign that the block could not be executed properly.

We forgot to define any input sequence for the block Add rois (the input is “null” says the error message). Note also the white cross over a red disk in the upper right corner of the block.

Experiment with the protocol to reproduce the error and answer the questions below.

Note that you surely don’t want to process a folder with 100 images each time you troubleshoot your protocol or go through 7 steps before observing the error. If your protocol is complex, isolate a minimal group of blocks surrounding the blocks that are causing the issue and play only with these blocks. You can save intermediate images and ROIs to use them as input to your minimal workflow.

  • Did you reset the blocks before running the protocol? We recommend to always reset, unless some blocks take a very long time to process. This avoids keeping old wrong results.
  • Did you select a sequence (an image) as input of your protocol?
A common mistake: not indicating the sequence to process in a protocol block.
  • Did you check all the input and output file paths? If you open a protocol written by someone else, it is likely that the paths are not correct. To check the outputs from a block, use the Display block (right click in the background of the protocol -> Display, or search for the block in the panel on the left of the Protocol Editor)

 

The display block is convenient to check the output of the blocks.
  • Are all the blocks connected to the correct inputs and outputs?
  • Is the execution order of the blocks ok? Sometimes a block gets by accident the wrong position in the protocol. When you run the protocol, it tries to execute this block first but it fails, because its input variable depends on a block that is not yet executed. The order of execution is given by the number in the upper right corner of the block.

Your script is giving you an error message or producing a different output than what you expect.

Read the error message if there is one. Identify the lines of code causing the issue. As for the protocols, if your code is complex, isolate a minimal group of lines producing the error. Check that all the variables are defined, that names of variables, functions… are consistent over your code, check also the length of objects (are you trying to select something at an index that does not exist?).

Ask your question on the image.sc forum

Despite all your efforts to read the documentation and troubleshoot the problem by yourself, you are still needing help.

We recommend to open a new thread on the image.sc forum with the tag “icy”. Please read the guidelines and the FAQ of the forum before posting and make sure a similar topic is not already opened. On the image.sc forum, you are asking the bioimage analysis community, and in particular the Icy users and developers. Keep in mind that all people answering there are doing it on their free time. You might have to wait a couple of days to get an answer, especially during holiday periods (Christmas, summer break…).

We encourage the discussion to stay public. If you encounter a certain issue, others will encounter it as well. By leaving a trace of your discussions on the forum, you are adding documentation for the community and your future self. Open discussions also give the possibility to anyone to contribute (mention that they encounter the same issue, provide help or share opinions for instance) and strengthen the community of users and developpers.

When creating a topic related to the Icy software on the image.sc forum, don’t forget to add the tag “icy”.

In your thread, provide as much information as possible to give the possibility to helpers to reproduce your issue. All the information you gathered while reading the documentation and troubleshooting your issue are precious, don’t forget to share them with others. If you have several questions, make separated threads.

Use the following categories for the following topics:

  • “Image Analysis” -> general questions on how to analyse an image
  • “Usage & Issues” -> issues with a plugin, bug report
  • “Development” -> feature request

Here is a check list of information you should provide:

  • What is your biological question? Don’t hesitate to share an annotated image pointing at structures of interest for you.
  • What is your bioimage analysis strategy? Thresholding, segmentation with HK-Means/watershed/active contours, tracking…?
  • An example image, representative of your images dataset (neither the best, nor the worse) in a raw format (no .png, no .jpeg, prefer the format given by your microscope)
  • The tool(s) you used with their version (Icy version 2.1.0.0, plugin HK-Means version…). If you are using a protocol, upload the .protocol file. If you use a plugin, provide the parameters you used to process the example image.
Always provide the version of Icy and the version of each plugin you have issue with.
  • A copy of the error message or log content (output tab, in the side panel)
Copy the message from the Output tab and/or provide screenshots of bug reports. Note that bug reports are sent directly to the authors of the plugin, not necessarily to the Icy team.

If, after around 10 days no one answered your question:

  • Add details, try to rephrase your issue
  • Contact by email the authors of the plugin or protocol block that is causing your issue and invite them to join you on the image.sc forum (to keep the discussion public). The authors of a plugin are listed on the documentation page of the plugin, click on their name to see their email address. Often, blocks share the same name as their parent plugin. In this case, contact the authors of the parent plugin. If your question is more general, please contact the Icy team by email, indicating the link to the thread you opened on the image.sc forum.

Leave a Review Cancel reply

You must Register or Login to post a review.

Leave a review
Cancel review

Welcome

Welcome to the Icy community support.

View Forum

Google Group

We’re migrating to a new Forum ⚡️, but if you need to access the old Google Group, please follow this link. All new topics should be opened here from now.

Latest Articles

  • Creating an Icy plugin with EzPlug
  • Creating blocks for Icy protocols
  • Installation instructions for Icy software
  • Code of Conduct
  • Icy cheat sheets
Icy is founded by
Institut Pasteur
France BioImaging
Resources
Plugins Protocols Scripts
Get Involved
Contributors Information Trainings Join Icy
Support
Forum Articles FAQ Ask for help
About
Aknowledgements Bioimage Analysis Contributors Privacy Policy
Credits
Designed by Yhello
contact
Yhello is a digital creation agency based in Paris, created by former scientists passionate about the web.
We use cookies on our website to give you the most relevant experience by remembering your preferences and repeat visits. By clicking “Accept All”, you consent to the use of ALL the cookies. However, you may visit "Cookie Settings" to provide a controlled consent.
Cookie SettingsAccept All
Manage consent

Privacy Overview

This website uses cookies to improve your experience while you navigate through the website. Out of these, the cookies that are categorized as necessary are stored on your browser as they are essential for the working of basic functionalities of the website. We also use third-party cookies that help us analyze and understand how you use this website. These cookies will be stored in your browser only with your consent. You also have the option to opt-out of these cookies. But opting out of some of these cookies may affect your browsing experience.
Necessary
Always Enabled
Necessary cookies are absolutely essential for the website to function properly. These cookies ensure basic functionalities and security features of the website, anonymously.
CookieDurationDescription
cookielawinfo-checkbox-analytics11 monthsThis cookie is set by GDPR Cookie Consent plugin. The cookie is used to store the user consent for the cookies in the category "Analytics".
cookielawinfo-checkbox-functional11 monthsThe cookie is set by GDPR cookie consent to record the user consent for the cookies in the category "Functional".
cookielawinfo-checkbox-necessary11 monthsThis cookie is set by GDPR Cookie Consent plugin. The cookies is used to store the user consent for the cookies in the category "Necessary".
cookielawinfo-checkbox-others11 monthsThis cookie is set by GDPR Cookie Consent plugin. The cookie is used to store the user consent for the cookies in the category "Other.
cookielawinfo-checkbox-performance11 monthsThis cookie is set by GDPR Cookie Consent plugin. The cookie is used to store the user consent for the cookies in the category "Performance".
viewed_cookie_policy11 monthsThe cookie is set by the GDPR Cookie Consent plugin and is used to store whether or not user has consented to the use of cookies. It does not store any personal data.
Functional
Functional cookies help to perform certain functionalities like sharing the content of the website on social media platforms, collect feedbacks, and other third-party features.
Performance
Performance cookies are used to understand and analyze the key performance indexes of the website which helps in delivering a better user experience for the visitors.
Analytics
Analytical cookies are used to understand how visitors interact with the website. These cookies help provide information on metrics the number of visitors, bounce rate, traffic source, etc.
Advertisement
Advertisement cookies are used to provide visitors with relevant ads and marketing campaigns. These cookies track visitors across websites and collect information to provide customized ads.
Others
Other uncategorized cookies are those that are being analyzed and have not been classified into a category as yet.
SAVE & ACCEPT