Version: V1.0.3
- Introduction
- Getting Started
- Navigating the Interface
- Setting Panel
- Results Panel
- Basic Project Walk Through
- Youtube Tutorials
- Advanced Features
- Using '*.ome.tiff' as image format
- Troubleshooting and Support
- Getting Help
- Appendix
- License
VISION is a sophisticated software tool specifically designed to analyze and process biological and microscopic images. With its user-friendly interface and powerful backend, it simplifies the complexities involved in image analysis, making it an indispensable resource for researchers, biologists, and educators alike.
The primary aim of VISION is to provide an intuitive yet powerful platform for the analysis of high-resolution image data. Whether it's for academic research, pharmaceutical developments, or educational purposes, VISION streamlines the process of extracting meaningful insights from intricate images, facilitating advancements in scientific understanding and applications.
- Advanced Image Processing: Equipped with state-of-the-art algorithms for image enhancement, segmentation, and filtering, ensuring high-quality analysis outputs.
- Object Detection and Quantification: Features robust tools for identifying and measuring various characteristics of objects within images, such as area, perimeter, and intensity.
- Customizable Workflows: Offers flexibility in analysis procedures, allowing users to adjust parameters and apply different analytical techniques to suit specific research needs.
- Multi-Dimensional Imaging Support: Capable of handling 2D, 3D, and time-lapse images, accommodating a wide range of scientific imaging requirements.
- Comprehensive Data Visualization and Export: Integrates visualization tools for immediate analysis result review and supports exporting data in multiple formats for further analysis or reporting.
- Plugin Architecture for Enhanced Functionality: Allows for the integration of custom plugins, extending the software's capabilities to meet unique analysis demands (Python script only).
VISION stands as a bridge between complex image analysis tasks and actionable scientific insights, embodying a blend of accessibility, precision, and comprehensiveness designed to empower users across various scientific fields.
The target audience for VISION encompasses a diverse group of individuals and professionals in fields where biological and microscopic image analysis plays a crucial role. The software is designed with features and functionalities that cater to the needs of:
- Researchers and Scientists: Individuals involved in biological, medical, and material science research who require detailed analysis of microscopic images to support their experiments and findings.
- Biologists and Bioinformaticians: Professionals who study cellular structures, functions, and processes, needing advanced tools to quantify and analyze biological data obtained from various imaging techniques.
- Educators and Academics: Teachers and lecturers in universities and colleges who require image analysis software for educational purposes, demonstrating concepts in cell biology, histology, and related fields to students.
- Medical Professionals: Pathologists, clinicians, and other healthcare providers who utilize microscopic imaging for diagnostics, research, and understanding disease mechanisms at the cellular and molecular levels.
- Pharmaceutical and Biotechnology Companies: R&D departments that focus on drug discovery, development, and quality control, where microscopic image analysis is essential for understanding compound effects and ensuring product quality.
- Graduate and Postgraduate Students: Students pursuing advanced degrees in fields such as biology, biomedical engineering, and materials science who need to analyze and interpret image data as part of their thesis or research projects.
- Imaging Specialists and Technologists: Individuals specializing in the operation of microscopic imaging equipment and the analysis of imaging data, looking for robust software to enhance image quality and extract relevant information.
This diverse audience benefits from VISION's ability to process and analyze complex imaging data accurately, making it an invaluable tool for advancingscientific research, education, and professional practice.
- Operating System: Windows 7 or later, macOS 10.13 (High Sierra) or later, Linux (Ubuntu 16.04 or later, CentOS 7 or later). These are general guidelines; VISION should run on any system where Python is supported.
- Python Version: Python 3.6 or newer. It's essential to have a compatible Python version for the software's dependencies.
- Memory (RAM): A minimum of 4 GB RAM, although 8 GB or more is recommended for processing large images or datasets.
- Processor: Intel Core i5 or equivalent, with at least 2 GHz processing speed. More advanced processors (i7, i9, or equivalent) can significantly improve performance, especially for computationally intensive tasks.
- Hard Disk Space: At least 1.5 GB of free space for installation, with additional space required for storing image data and analysis results.
These requirements are provided as a general guideline based on typical software dependencies and the performance needs of image analysis tasks. Users with specific or advanced usage scenarios (e.g., handling very large datasets, 3D imaging, time-lapse analyses) might require more powerful hardware. We encourage users to consider their particular needs and consult with their IT department or professionals when setting up systems for VISION. Additionally, future versions of the software or updates to dependencies may alter these requirements.
Please note that these system requirements are based on general expectations for software of this nature and have not been rigorously tested across all platforms. Performance can vary based on the specific hardware and software environment, size and complexity of the data being processed, and specific tasks being performed. We welcome feedback from our user community to help refine these recommendations over time.
VISION is designed to be easily accessible, offering both a standalone version for a straightforward installation across Windows, macOS, and Linux, as well as a Python-based version for advanced users or developers. Below are the steps to get started with either version.
General Steps for All Platforms:
- Download the lates VISION Version for your respective operating system (Windows, macOS, or Linux) from the VISION official website (https://github.com/biosciflo/VISION/releases).
- Extract the ZIP file to your desired location. This will create a folder containing the VISION executable and all necessary dependencies.
- Navigate to the extracted folder and double-click on
VISION.exeto start the application.
- Open the extracted folder, find the
VISION.appfile, and double-click to launch it. If you encounter any security prompts preventing the app from opening (due to macOS Gatekeeper), right-click (or Control-click) the app and select Open, then confirm in the dialog #
Quick Guide for Running Blocked Applications on macOS
macOS prevents certain applications from running due to security restrictions, particularly those downloaded from the internet and not signed by a verified developer.
Step 1: Grant Execution Permission
- Command:
chmod +x /path/to/VISION(the folder)/VISION(theapp) - Purpose: Grants execute permission to your application, making it runnable on your system.
- Usage: Replace
/path/to/VISION(the folder)/VISION(theapp)with the actual path to the application you wish to run.
Step 2: Remove Quarantine Attribute
- Command:
xattr -cr /path/to/VISION(the folder) - Purpose: Removes the quarantine attribute macOS applies to files downloaded from the internet, which causes the security block.
- Usage: Replace
/path/to/VISION(the folder)with the path to the affected application and folder (_internal) containing multiple blocked files.
Notes
- These steps are particularly useful for applications blocked by macOS due to lack of a verified developer signature or for files marked as unsafe because they were downloaded from the internet.
- Always ensure you trust the source of the software you're attempting to run, as bypassing these protections can expose your system to risks.
- This guide is intended to help users quickly resolve issues with running applications that macOS has blocked due to its security settings.
Linux(Not supported yet):
- Open a terminal and change to the directory containing the extracted files.
- Make the VISION binary executable with the command:
chmod +x VISION(replaceVISIONwith the actual name of the binary file). - Run the application by typing
./VISIONin the terminal.
For those who prefer the flexibility of a Python environment or wish to integrate VISION into their existing workflows, follow these general steps:
- Ensure Python is Installed: VISION requires Python 3.6 or newer. If you don't have Python installed, download it from https://www.python.org/.
- Install Dependencies: Some Python packages are required to run VISION. Install them using pip by running
pip install -r requirements.txtin your terminal or command prompt, assuming arequirements.txtfile is provided with the necessary package names. - Download and Run VISION: Download the VISION Python scripts and run them in your preferred Python environment or IDE.
Additional Resources:
- Python Official Documentation: https://docs.python.org/3/using/index.html
- pip Documentation: https://pip.pypa.io/en/stable/user_guide/
- IDE Recommendations: Consider using an IDE such as PyCharm, Visual Studio Code, Spyder, or Jupyter Notebooks for a more integrated development experience.
Note The standalone version simplifies the installation process by bundling the application with all its dependencies. It's ideal for users who prefer a quick setup without the need to manually install Python or additional packages. For detailed guides on using Python and managing packages, refer to the provided additional resources.
Welcome to VISION! As you start the application for the first time, here's what you can expect and how to navigate the initial setup process.
What to Expect:
- Console Window: Upon launching VISION, a console window will appear. This window is an essential part of the application, providing real-time feedback, status updates, and information about the tasks being performed. It's normal for this console to remain open throughout your use of VISION, as it will display valuable information during the application's run.
- Splash Screen (Windows Only): Shortly after the console window opens, you'll be greeted by a splash screen. This splash screen serves as a visual indicator that VISION is in the process of starting up. It's designed to provide a friendly welcome while the application loads the necessary components in the background.
- Initial Loading Time: The first startup of VISION may take some time, which is completely normal and depends on your system's specifications. This initial loading allows VISION to properly initialize and prepare for optimal performance. We appreciate your patience during this process.
- GUI Appearance: Once initialization is complete, the main graphical user interface (GUI) of VISION will appear. This is where you will interact with the software to load images, perform analyses, and view results. The GUI is designed to be user-friendly and intuitive, providing easy access to all of VISION's powerful features.
- Console Window During Use: As mentioned, the console window will remain open while you use VISION. It will continue to provide important messages and updates. Keeping an eye on the console can offer insights into the application's processes and alert you to any actions required on your part.
Getting Started: With the GUI open, you are now ready to begin exploring VISION. Whether you're analyzing your first image or configuring settings for your analysis, VISION is equipped to support your work.
A Note on Performance: The performance and responsiveness of VISION after the initial launch will vary based on the complexity of the tasks you're performing and your computer's hardware. For demanding tasks or large datasets, enhanced system specifications can contribute to smoother operation.
Welcome to VISION! This section will help you become familiar with the main window's interface, ensuring you can navigate the software efficiently and make the most out of its powerful features.
The main window of VISION is designed with intuitiveness and efficiency in mind, structured to facilitate easy access to all necessary tools and functionalities for comprehensive image analysis. Here's what you'll find:
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Settings Panel (2): Positioned to maximize ease of access, the Settings Panel is where you'll begin your journey with VISION. From top to bottom, it comprises:
- Load and Table Interaction Section: At the very top, this area allows you to load images into VISION. Following image loading, the section provides functionalities for interacting with the list (table) of loaded images, making it easier to manage and select specific datasets for analysis.
- Table for Loaded Images: Directly below the interaction tools, this table displays all your loaded images. It serves as a central hub for selecting and organizing your analysis queue, providing an overview of your working datasets.
- Test Run and Analysis Settings: Moving down, this segment of the Settings Panel is dedicated to preparing and initiating your image analyses. Here, you can conduct preliminary tests, run analyses, and adjust general settings that apply to the upcoming analysis tasks.
- Specific Analysis Settings: This section is tailored for fine-tuning the analysis parameters, including:
- Membrane Settings: Adjustments specific to analyzing membrane-related features.
- Cytosol Settings: Settings for analyzing cytosolic components.
- Advanced Settings: Additional parameters for users requiring more control and customization of the analysis process.
- Savings Settings: Options for determining how and where your analysis results are saved.
- Mini Console: Located at the bottom of the Settings Panel, the mini console serves as an interactive feedback area. It displays important user messages, warnings, and recommendations, especially useful if a setting is not correctly configured.
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Results Panel (3): This panel is your destination for viewing the outcomes of your analyses. It is organized into three main tabs, each offering a different perspective on your results:
- Mask Results: Displays the results related to image segmentation or masking, providing insights into the specific areas of interest within your images.
- Full Image Results: Offers a holistic view of the analyzed images, highlighting the overall findings and annotations made by the software.
- Object Results: Focuses on the results at the object level, detailing measurements, classifications, and other quantitative data extracted from individual objects identified in your images.
- Load Files: Load one or multiple images (*.lsm, *.czi, *.ome.tiff).
- Load Folder: Loads all images in folder with compatible file formats (*.lsm, *.czi, *.ome.tiff).
- Clear Selection: Clears (unselects a selected item) in image table.
- Delete Entry: Deletes selected item in image table.
- Clear Table: Clears (deletes) full image table.
- Test Mask: Runs the thresholding and masking part of the algorithm and returns the results.
- Run Analysis: Runs the full Analysis with the selected sub-options.
- Object Detection: Enables/disables Object Detection for the full analysis.
- Linearization: Enables/disables object Linearization for the full analysis. (Enabling Object Detection is mandatory)
- Channel Settings: Upon loading image files, fields A, B, C, & D automatically populate with existing channel information, such as '488' or numbers '1-9', derived directly from the original file's metadata. When loading spectral LSM or CZI files, the results in the comboboxes will include all available channel wavelengths.
- Membrane Profiler: Enables/disables Membrane Profiler.
- Colocalization: Enables/disables an additional, independent colocalization channel. The population of the combobox below follows the same procedure as described in Channel Settings above.
- Equation: The "Equation" text field leverages the channel settings A, B, C, and D to calculate the β-Value, for example, the GP-Value using the formula “(A-B)/(A+B)”. Please note, only the variables A, B, C, and D are permitted in this field.
- Thresholding Options – Specific Channel: Enable/disable the specific channel Thresholding. Uses combobox next to select the channel dedicated to Thresholding (if disabled: default thresholding is used – Channel with lowest intensity used in equation).
- Thresholding Options – Thresholding Mode: Choose between Automatic Otsu Algorithm or Manual. (if Manual, Manual Cutoff Level is enabled).
- Thresholding Options – Manual Cutoff Level: Enter an Intensity Value as the Cutoff Level for Thresholding.
- Thresholding Options – Signal to Noise Ratio: Enter Signal to Noise Ratio for Thresholding algorithm.
- Thresholding Options – Background Compensation: Enable/disable Background Compensation mode for the Thresholding algorithm. When enabled, it allows for the adjustment of Background Mean and Standard Deviation through manual modifications. (as well as through “Probe Raw Image”- Probe Raw Image is in the MASK Results Tab, click on button Probe Raw Image and raise a square area of interest (e.g. Background). Mean, median Standard deviation, min & max will be calculated of this area and shown below, additionally, the mean and standard deviation values will be automatically updated as the "Background Mean" and "Background Std" in the Thresholding options.)
- Masking Options – Compression: Enable/disable Compression and Compression Value (float).
- Masking Options – Remove Object: Enable/disable Remove Objects and Remove Objects Value (int).
- Masking Options – Fill Holes: Enable/disable Fill Holes and Fill Holes Value (float).
- Masking Options – Gaussian Filter: Enable/disable Gaussian Filter and Gaussian Filter Value (float).
- Masking Options – Dilation: Enable/disable Dilation, Dilation Shape, and X/Y Dimensions of Dilation Shape (int).
- Binning: Min/Max/Width of Binning.
- All Settings as described for the membrane part, but it is performed on the cytosolic regions.
- Cytosolic Measurement: Enable/disable the analysis of cytosolic regions.
- Object Segmentation – Skeleton Debranching
- Object Segmentation – tol0
- Object Segmentation – tol1
- Membrane Profiling – Recentering: Enable/disable Recentering of Integration Element
- Membrane Profiling – dim_line
- Membrane Profiling – Integrations Element: Integration Element Shape
- Membrane Profiling – Integrations Element X/Y-Dimension: Integration Element XY Dimension
- Membrane Profiling – β-Value Threshold Auto Cut off
- Select Saving Path: Choose a different path to save Results (default: path of image)
- Save cropped Membrane: Save membrane images of individual detected objects.
- Save cropped Cytosol: Save cytosolic imagesof individual detected objects.
- Save Linearized Cytosol: Save linearized images of individual detected objects.
- Save Phasors: Save Phasor plots in excel.
- Save Settings in JSON: Save used settings in a dedicated JSON File.
- Save Results in JSON: Save used settings and all results in a dedicated JSON File.
Each panel has a Membrane and Cytosolic part and is split into Mask, Full Image, & Object Results Panel.
- Start VISON
- Load File(s) / Load Folder
- Inspect RawImage Inspect all channels and dimensions of your RawImage by clicking onto the Filename in the image table.
- (Membrane Settings) (Optional) Enter Equation for β-Value calculation.
- (Membrane Settings) Select Channels for each used variable in Equation.
- (Membrane Settings) (Optional) Enable and Choose Specific Thresholding Channel.
- Test Mask (if Mask is not optimal follow with Steps a-c, otherwise go to 7) a. Move displayed Raw Image (Right Panel of Mask Results) to the channel of Choose Specific Thresholding Channel or used Channel of Equation with the lowest intensity. Click on “Probe Raw Image” and select a background area. b. Activate Background Compensation. c. Test Mask (if Mask is not optimal follow with Steps d-, otherwise go to 7) d. Enable options such as the Gauss Filter, Dilation, Compression, and Fill Holes, then fine-tune their respective parameters until the mask is satisfactory. Proceed to Step 7 upon completion.
- Run Analysis – (Full Image) a. Check Full Image Results.
- Activate Object Detection
- Run Analysis – (Full Image & Object Detection) a. If an error appears in the mini console, try to adapt the Masking options; it could be that the subroutines can't detect single objects. b. Check Full Image Results and Object-Related Results.
Note: Once you have run the image, all Results are automatically Saved.
- TUTORIAL1 - VISION BASIC TUTORIAL
- TUTORIAL2 - Image analysis via VISION
- TUTORIAL3 - Working with .ome.tif images in VISION
- Custom Analyses: (cooming soon)
- Patch Processing: If multiple images are in the Image – List, either:
- Select Multiple Images and press Run – Selected Images will be Processed. Or…
- Press “Clear Selection” and Press Run - All Images in list will be Processed.
- Detailed Masking Options: VISION provides flexible thresholding and masking capabilities. Each masking option available in the global settings is also accessible for individual customization within the "Detailed Masking Options" table (available for membrane and cytosolic part). This level of detail ensures that each slice can be analyzed with precision, accommodating both 3D stacks and time-lapse sequences. Here's how you can customize these settings:
- Time-Lapse Sequences: For datasets organized by time, the "Detailed Masking Options" table expands dynamically, adding a column for each time point. This feature allows for the adjustment of masking settings uniquely for each time point.
- 3D Stacks: For spatial (z) slices within a 3D stack, use the dedicated combobox to select the specific time point (T Position) you wish to customize. This selection enables targeted modification of the masking options for individual z-layers.
- Important Note for Batch Processing: To apply specific masking options across multiple images in batch processing, it is essential to first initialize the detailed masking settings for each image file listed in the image table. This involves clicking on each file to activate the detailed options. Failing to perform this step may result in a key value error displayed in the mini console. We are aware of this issue and plan to streamline the process in future updates of VISION.
Currently image file types of '.lsm' and '.czi' can be openend but with '*.ome.tiff' (imagej/fiji) all images can be anlaysed with VISION.
- Other image types: If you have special image types such as .lif or .obf. Please get in touch with us. We will be happy to implement the image type if you can provide us with some test images.
-
(1) First open FIJI/ImageJ
-
(2) Load image file as Hyperstack
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(3) Select "Save" as "OME-TIFF..."
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(4) Enter Filename with the ending '*.ome.tif' (e.g. test.ome.tif)
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(5) Choose Filetype OME-TIFF
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(6) Press save
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(7) if Window with multiple options for T,Z and Channesl appear do not select anything, just press OK.
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(8) Deselect ROIs, Use "Uncompressed" and press OK
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ADD: This can be done with all kind of images supported by VISION or not. e.g LIF files are currently not supported with an export as '*.ome.tif' you export Sinle Sceens form a LIF project.
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Glossary: Definitions of terms and concepts used within the guide and software.
- Metadata: Ensure that all relevant metadata is recorded, including details about the imaging setup, sample preparation, and acquisition settings. This includes the type of microscope, objective lenses, exposure times, and light sources used.
- Calibration: Maintain consistent calibration of imaging systems to ensure reproducibility. Include calibration scales or indicators in the images.
- Transparency: Provide information on the software and settings used for image analysis to allow for reproducibility and transparency.
- Photon Noise Management: Maximize photon detection by optimizing exposure times and minimizing background noise through appropriate use of detector apertures and cooling techniques for CCD cameras.
- Dark and Read Noise: Reduce thermal noise by cooling the camera sensor and minimize read noise by using high-performance cameras designed for low-light imaging.
- Sampling Rates: Use appropriate sampling rates to ensure that the pixel size is suitable for the resolution of the microscope. The Nyquist criterion suggests that the pixel size should be at least half the size of the optical resolution limit.
- Contrast and Brightness: Adjust contrast and brightness appropriately without over-processing the images. Maintain the original data integrity to allow for proper interpretation and analysis.
- Image Restoration: Implement deconvolution and other image restoration techniques to improve image clarity while maintaining the original information content.
- Calibration: Regularly check and maintain the calibration of the microscope and imaging system. Include a troubleshooting section in your manual to address common issues such as focus drift, alignment problems, and illumination inconsistencies.
- Artifact Recognition: Provide example images and descriptions of common artifacts and how to avoid or correct them. This can help users recognize and troubleshoot problems in their own imaging setups.
- Community Guidelines: Follow established community guidelines, such as those from the QUAREP-LiMi initiative, which provides detailed checklists and protocols for quality assessment and reproducibility in light microscopy. These guidelines cover a wide range of aspects from data acquisition to image analysis and publication standards.
- Data Sharing: Encourage users to share their data and analysis pipelines in public repositories to promote transparency and reproducibility in the scientific community.
- EMBL Guidelines for Microscopy Images
- QUAREP-LiMi Guidelines
- Minimum Information Guidelines for Fluorescence Microscopy
Issue: The VISION software does not install correctly.
Potential Causes:
- Incompatible operating system or hardware.
- Missing dependencies.
Solutions:
- Ensure your system meets the minimum requirements listed in the installation guide.
- Follow the installation steps carefully, and ensure all necessary dependencies are installed.
- Refer to the installation section for detailed instructions.
Issue: The software crashes or becomes unresponsive during use.
Potential Causes:
- Insufficient system resources (RAM, CPU).
- Bug in the software.
Solutions:
- Close other applications to free up system resources.
- Ensure your system meets the recommended hardware specifications.
- Check for software updates that may address stability issues.
- Report the issue on our ISSUES with detailed information about your system and the problem. (How to report: Reporting Bugs)
Issue: You encounter error messages while using the software.
Potential Causes:
- Incorrect usage or unsupported operations.
- Missing or corrupt files.
Solutions:
- Refer to the error message documentation in the manual or on our Error Messages and Solutions to understand the cause and potential fixes.
- Ensure all required files are present and correctly formatted.
Issue: The software produces unexpected or incorrect results.
Potential Causes:
- Incorrect input data or parameters.
- Misconfigured settings.
- Bug in the software.
Solutions:
- Verify that your input data meets the software's requirements.
- Double-check all parameters and settings before running the software.
- Refer to the user manual for guidance on proper usage and configuration.
- Report the issue on our ISSUES with detailed information about your system and the problem. (How to report: Reporting Bugs)
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Error Message:
Error: Invalid character '{char}' found in the text. ('E', 'I', 'N', 'O', 'Q', 'S' are reserved for mathematical operators). Please use A,B,C or D.- Cause: Invalid character found in the input string.
- Solution: Ensure that only characters A, B, C, and D are used in the input string.
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Error Message:
Error: Invalid letter '{char}' found in the text.- Cause: Invalid uppercase letter found in the input string.
- Solution: Ensure only A, B, C, and D are used as uppercase letters.
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Error Message:
Error Membrane Settings: Letter(s) {chars} are in use in the Equation, but corresponding ComboBox value(s) are not selected. Please select a Channel for {chars}- Cause: ComboBox values for certain letters (A,B,C,D) are not selected.
- Solution: Select the appropriate ComboBox (A,B,C,D) values for the letters used in the equation.
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Error Message:
Error Membrane Settings: Letter(s) {chars} are not 'NaN' but corresponding letter(s) are not used in the equation. Please select 'NaN' for {chars}- Cause: ComboBox (A,B,C,D) values are not 'NaN' while the corresponding letters are not used in the equation.
- Solution: Set the ComboBox (A,B,C,D) values to 'NaN' for the letters not used in the equation.
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Error Message:
Error: It was not possible to detect single objects. Please check your masking and thresholding settings.- Cause: Function DBSCAN found no samples or no objects to concatenate.
- Solution: Review and adjust the masking and thresholding settings.
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Error Message:
Invalid value. Expected 'NAN'.- Cause: Value conversion failed, and the value was not 'NAN'.
- Solution: Ensure the value is either valid or 'NAN' as expected.
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Error Message:
The value '{newValue}' is not valid for 'Thresholding Mode'. (Otsu or Manual)- Cause: Invalid value for Thresholding Mode.
- Solution: Use either 'Otsu' or 'Manual' for Thresholding Mode.
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Error Message:
The value '{newValue}' is not valid for 'Manual Cutoff Level'. (a int)- Cause: Non-integer value for Manual Cutoff Level.
- Solution: Enter an integer value for Manual Cutoff Level.
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Error Message:
The value '{newValue}' is not valid for 'Compression True/False'. (True or False)- Cause: Invalid value for Compression True/False.
- Solution: Use either 'True' or 'False' for Compression.
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Error Message:
The value '{newValue}' is not valid for 'Compression Value'. (a float)- Cause: Non-float value for Compression Value.
- Solution: Enter a float value for Compression Value.
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Error Message:
The value '{newValue}' is not valid for 'Remove Object'. (NaN or a int)- Cause: Value for Remove Object is neither 'NaN' nor an integer.
- Solution: Use either 'NaN' or an integer for Remove Object.
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Error Message:
The value '{newValue}' is not valid for 'Fill Holes'. (NaN or a float)- Cause: Value for Fill Holes is neither 'NaN' nor a float.
- Solution: Use either 'NaN' or a float for Fill Holes.
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Error Message:
The value '{newValue}' is not valid for 'Dilate True/False'. (True or False)- Cause: Invalid value for Dilate True/False.
- Solution: Use either 'True' or 'False' for Dilate.
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Error Message:
The value '{newValue}' is not valid for 'Dilation Shape'. (octagon, disk or square)- Cause: Invalid value for Dilation Shape.
- Solution: Use either 'octagon', 'disk', or 'square' for Dilation Shape.
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Error Message:
The value '{newValue}' is not valid for 'Dilation Shape Dimension 1'. (a int)- Cause: Non-integer value for Dilation Shape Dimension 1.
- Solution: Enter an integer value for Dilation Shape Dimension 1.
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Error Message:
The value '{newValue}' is not valid for 'Dilation Shape Dimension 2'. (a int)- Cause: Non-integer value for Dilation Shape Dimension 2.
- Solution: Enter an integer value for Dilation Shape Dimension 2.
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Error Message:
The value "{newValue}" is not valid for "Filter Type". ( pls choose one of these: "No Filter", "Gaussian", "Mode", "Median", "Mean", "Geometric_mean","Majority","Minimum","Maximum","Sum","Gradient","Entropy")- Cause: Invalid value for Filter Type.
- Solution: Choose one of the valid filter types listed.
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Error Message:
The value '{newValue}' is not valid for 'Filter Value'. (a float)- Cause: Non-float value for Filter Value.
- Solution: Enter a float value for Filter Value.
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Error Message:
The value '{newValue}' is not valid for 'Signal to Noise Ratio'. (a float)- Cause: Non-float value for Signal to Noise Ratio.
- Solution: Enter a float value for Signal to Noise Ratio.
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Error Message:
The value '{newValue}' is not valid for 'Background StdDev'. (a float)- Cause: Non-float value for Background StdDev.
- Solution: Enter a float value for Background StdDev.
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Error Message:
The value '{newValue}' is not valid for 'Background Mean'. (NaN or a float)- Cause: Value for Background Mean is neither 'NaN' nor a float.
- Solution: Use either 'NaN' or a float for Background Mean.
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Error Message:
The value '{value}' is not valid for 'Specific Channel Wavelength'. (NaN or a list of available channels e.g. [488,647])- Cause: Invalid value for Specific Channel Wavelength.
- Solution: Use either 'NaN' or a list of available channels (e.g., [488, 647]) for Specific Channel Wavelength.
If you encounter any issues while using our software, we highly encourage you to report them on our ISSUES page so we can work on fixing them promptly. Here's how to report a bug on GitHub:
Visit the GitHub Repository: Navigate to our software's GitHub repository. If you're not already signed in, GitHub will prompt you to log in or create a new account.
Check Existing Issues: Before submitting a new bug report, please take a moment to check if the issue has already been reported. You can use the repository's search tool to find issues by keywords. If you find an existing issue that matches yours, you can add any new information you have to that issue rather than creating a new one.
Create a New Issue: If your issue is new, click the 'Issues' tab in the repository, and then click the 'New issue' button. If the repository uses issue templates, select the one that matches your situation or choose 'Open a blank issue' if none of the templates fit.
Fill Out the Issue Template: Provide a clear and concise title for your issue. Fill in the template with as much detail as possible. Be sure to include de following parts:
- A brief description of the issue.
- Steps to reproduce the issue.
- Expected behavior and what actually happens.
- Any relevant error messages or screenshots. For that please add the "global_error_log.txt" and/or "error_log.txt". They are in the folder were your executable file is located.
- Your operating system and version, as well as the software version you're using.
- Any files that you used.
- Submit the Issue: Once you've filled out the template, submit your issue by clicking the 'Submit new issue' button.
Monitor Your Issue: After submitting, keep an eye on your issue for any comments or questions from the development team. They may need more information or provide a workaround or solution.
Your reports play a crucial role in improving the quality of the software, and we appreciate your contributions to making our project better for everyone.
If you encounter issues not covered in this guide, please refer to the following resources:
- Support: Contact us for support via the ISSUES .
We hope this troubleshooting guide helps you resolve any issues and enhances your experience with the VISION software.
- FAQs: Answers to frequently asked questions about the software.
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for
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The licenses for most software and other practical works are designed
to take away your freedom to share and change the works. By contrast,
the GNU General Public License is intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users. We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors. You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
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Developers that use the GNU GPL protect your rights with two steps:
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TERMS AND CONDITIONS
0. Definitions.
"This License" refers to version 3 of the GNU General Public License.
"Copyright" also means copyright-like laws that apply to other kinds of
works, such as semiconductor masks.
"The Program" refers to any copyrightable work licensed under this
License. Each licensee is addressed as "you". "Licensees" and
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To "modify" a work means to copy from or adapt all or part of the work
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A "covered work" means either the unmodified Program or a work based
on the Program.
To "propagate" a work means to do anything with it that, without
permission, would make you directly or secondarily liable for
infringement under applicable copyright law, except executing it on a
computer or modifying a private copy. Propagation includes copying,
distribution (with or without modification), making available to the
public, and in some countries other activities as well.
To "convey" a work means any kind of propagation that enables other
parties to make or receive copies. Mere interaction with a user through
a computer network, with no transfer of a copy, is not conveying.
An interactive user interface displays "Appropriate Legal Notices"
to the extent that it includes a convenient and prominently visible
feature that (1) displays an appropriate copyright notice, and (2)
tells the user that there is no warranty for the work (except to the
extent that warranties are provided), that licensees may convey the
work under this License, and how to view a copy of this License. If
the interface presents a list of user commands or options, such as a
menu, a prominent item in the list meets this criterion.
1. Source Code.
The "source code" for a work means the preferred form of the work
for making modifications to it. "Object code" means any non-source
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A "Standard Interface" means an interface that either is an official
standard defined by a recognized standards body, or, in the case of
interfaces specified for a particular programming language, one that
is widely used among developers working in that language.
The "System Libraries" of an executable work include anything, other
than the work as a whole, that (a) is included in the normal form of
packaging a Major Component, but which is not part of that Major
Component, and (b) serves only to enable use of the work with that
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implementation is available to the public in source code form. A
"Major Component", in this context, means a major essential component
(kernel, window system, and so on) of the specific operating system
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produce the work, or an object code interpreter used to run it.
The "Corresponding Source" for a work in object code form means all
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programs which are used unmodified in performing those activities but
which are not part of the work. For example, Corresponding Source
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such as by intimate data communication or control flow between those
subprograms and other parts of the work.
The Corresponding Source need not include anything that users
can regenerate automatically from other parts of the Corresponding
Source.
The Corresponding Source for a work in source code form is that
same work.
2. Basic Permissions.
All rights granted under this License are granted for the term of
copyright on the Program, and are irrevocable provided the stated
conditions are met. This License explicitly affirms your unlimited
permission to run the unmodified Program. The output from running a
covered work is covered by this License only if the output, given its
content, constitutes a covered work. This License acknowledges your
rights of fair use or other equivalent, as provided by copyright law.
You may make, run and propagate covered works that you do not
convey, without conditions so long as your license otherwise remains
in force. You may convey covered works to others for the sole purpose
of having them make modifications exclusively for you, or provide you
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not control copyright. Those thus making or running the covered works
for you must do so exclusively on your behalf, under your direction
and control, on terms that prohibit them from making any copies of
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Conveying under any other circumstances is permitted solely under
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No covered work shall be deemed part of an effective technological
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similar laws prohibiting or restricting circumvention of such
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You may convey verbatim copies of the Program's source code as you
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keep intact all notices of the absence of any warranty; and give all
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and you may offer support or warranty protection for a fee.
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You may convey a work based on the Program, or the modifications to
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terms of section 4, provided that you also meet all of these conditions:
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work need not make them do so.
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used to limit the access or legal rights of the compilation's users
beyond what the individual works permit. Inclusion of a covered work
in an aggregate does not cause this License to apply to the other
parts of the aggregate.
6. Conveying Non-Source Forms.
You may convey a covered work in object code form under the terms
of sections 4 and 5, provided that you also convey the
machine-readable Corresponding Source under the terms of this License,
in one of these ways:
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(including a physical distribution medium), accompanied by the
Corresponding Source fixed on a durable physical medium
customarily used for software interchange.
b) Convey the object code in, or embodied in, a physical product
(including a physical distribution medium), accompanied by a
written offer, valid for at least three years and valid for as
long as you offer spare parts or customer support for that product
model, to give anyone who possesses the object code either (1) a
copy of the Corresponding Source for all the software in the
product that is covered by this License, on a durable physical
medium customarily used for software interchange, for a price no
more than your reasonable cost of physically performing this
conveying of source, or (2) access to copy the
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c) Convey individual copies of the object code with a copy of the
written offer to provide the Corresponding Source. This
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only if you received the object code with such an offer, in accord
with subsection 6b.
d) Convey the object code by offering access from a designated
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Corresponding Source along with the object code. If the place to
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available for as long as needed to satisfy these requirements.
e) Convey the object code using peer-to-peer transmission, provided
you inform other peers where the object code and Corresponding
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A separable portion of the object code, whose source code is excluded
from the Corresponding Source as a System Library, need not be
included in conveying the object code work.
A "User Product" is either (1) a "consumer product", which means any
tangible personal property which is normally used for personal, family,
or household purposes, or (2) anything designed or sold for incorporation
into a dwelling. In determining whether a product is a consumer product,
doubtful cases shall be resolved in favor of coverage. For a particular
product received by a particular user, "normally used" refers to a
typical or common use of that class of product, regardless of the status
of the particular user or of the way in which the particular user
actually uses, or expects or is expected to use, the product. A product
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"Installation Information" for a User Product means any methods,
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and execute modified versions of a covered work in that User Product from
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code is in no case prevented or interfered with solely because
modification has been made.
If you convey an object code work under this section in, or with, or
specifically for use in, a User Product, and the conveying occurs as
part of a transaction in which the right of possession and use of the
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fixed term (regardless of how the transaction is characterized), the
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by the Installation Information. But this requirement does not apply
if neither you nor any third party retains the ability to install
modified object code on the User Product (for example, the work has
been installed in ROM).
The requirement to provide Installation Information does not include a
requirement to continue to provide support service, warranty, or updates
for a work that has been modified or installed by the recipient, or for
the User Product in which it has been modified or installed. Access to a
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Corresponding Source conveyed, and Installation Information provided,
in accord with this section must be in a format that is publicly
documented (and with an implementation available to the public in
source code form), and must require no special password or key for
unpacking, reading or copying.
7. Additional Terms.
"Additional permissions" are terms that supplement the terms of this
License by making exceptions from one or more of its conditions.
Additional permissions that are applicable to the entire Program shall
be treated as though they were included in this License, to the extent
that they are valid under applicable law. If additional permissions
apply only to part of the Program, that part may be used separately
under those permissions, but the entire Program remains governed by
this License without regard to the additional permissions.
When you convey a copy of a covered work, you may at your option
remove any additional permissions from that copy, or from any part of
it. (Additional permissions may be written to require their own
removal in certain cases when you modify the work.) You may place
additional permissions on material, added by you to a covered work,
for which you have or can give appropriate copyright permission.
Notwithstanding any other provision of this License, for material you
add to a covered work, you may (if authorized by the copyright holders of
that material) supplement the terms of this License with terms:
a) Disclaiming warranty or limiting liability differently from the
terms of sections 15 and 16 of this License; or
b) Requiring preservation of specified reasonable legal notices or
author attributions in that material or in the Appropriate Legal
Notices displayed by works containing it; or
c) Prohibiting misrepresentation of the origin of that material, or
requiring that modified versions of such material be marked in
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it) with contractual assumptions of liability to the recipient, for
any liability that these contractual assumptions directly impose on
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All other non-permissive additional terms are considered "further
restrictions" within the meaning of section 10. If the Program as you
received it, or any part of it, contains a notice stating that it is
governed by this License along with a term that is a further
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a further restriction but permits relicensing or conveying under this
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of that license document, provided that the further restriction does
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If you add terms to a covered work in accord with this section, you
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Additional terms, permissive or non-permissive, may be stated in the
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the above requirements apply either way.
8. Termination.
You may not propagate or modify a covered work except as expressly
provided under this License. Any attempt otherwise to propagate or
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this License (including any patent licenses granted under the third
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However, if you cease all violation of this License, then your
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provisionally, unless and until the copyright holder explicitly and
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holder fails to notify you of the violation by some reasonable means
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Moreover, your license from a particular copyright holder is
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violation by some reasonable means, this is the first time you have
received notice of violation of this License (for any work) from that
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your receipt of the notice.
Termination of your rights under this section does not terminate the
licenses of parties who have received copies or rights from you under
this License. If your rights have been terminated and not permanently
reinstated, you do not qualify to receive new licenses for the same
material under section 10.
9. Acceptance Not Required for Having Copies.
You are not required to accept this License in order to receive or
run a copy of the Program. Ancillary propagation of a covered work
occurring solely as a consequence of using peer-to-peer transmission
to receive a copy likewise does not require acceptance. However,
nothing other than this License grants you permission to propagate or
modify any covered work. These actions infringe copyright if you do
not accept this License. Therefore, by modifying or propagating a
covered work, you indicate your acceptance of this License to do so.
10. Automatic Licensing of Downstream Recipients.
Each time you convey a covered work, the recipient automatically
receives a license from the original licensors, to run, modify and
propagate that work, subject to this License. You are not responsible
for enforcing compliance by third parties with this License.
An "entity transaction" is a transaction transferring control of an
organization, or substantially all assets of one, or subdividing an
organization, or merging organizations. If propagation of a covered
work results from an entity transaction, each party to that
transaction who receives a copy of the work also receives whatever
licenses to the work the party's predecessor in interest had or could
give under the previous paragraph, plus a right to possession of the
Corresponding Source of the work from the predecessor in interest, if
the predecessor has it or can get it with reasonable efforts.
You may not impose any further restrictions on the exercise of the
rights granted or affirmed under this License. For example, you may
not impose a license fee, royalty, or other charge for exercise of
rights granted under this License, and you may not initiate litigation
(including a cross-claim or counterclaim in a lawsuit) alleging that
any patent claim is infringed by making, using, selling, offering for
sale, or importing the Program or any portion of it.
11. Patents.
A "contributor" is a copyright holder who authorizes use under this
License of the Program or a work on which the Program is based. The
work thus licensed is called the contributor's "contributor version".
A contributor's "essential patent claims" are all patent claims
owned or controlled by the contributor, whether already acquired or
hereafter acquired, that would be infringed by some manner, permitted
by this License, of making, using, or selling its contributor version,
but do not include claims that would be infringed only as a
consequence of further modification of the contributor version. For
purposes of this definition, "control" includes the right to grant
patent sublicenses in a manner consistent with the requirements of
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Each contributor grants you a non-exclusive, worldwide, royalty-free
patent license under the contributor's essential patent claims, to
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In the following three paragraphs, a "patent license" is any express
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(such as an express permission to practice a patent or covenant not to
sue for patent infringement). To "grant" such a patent license to a
party means to make such an agreement or commitment not to enforce a
patent against the party.
If you convey a covered work, knowingly relying on a patent license,
and the Corresponding Source of the work is not available for anyone
to copy, free of charge and under the terms of this License, through a
publicly available network server or other readily accessible means,
then you must either (1) cause the Corresponding Source to be so
available, or (2) arrange to deprive yourself of the benefit of the
patent license for this particular work, or (3) arrange, in a manner
consistent with the requirements of this License, to extend the patent
license to downstream recipients. "Knowingly relying" means you have
actual knowledge that, but for the patent license, your conveying the
covered work in a country, or your recipient's use of the covered work
in a country, would infringe one or more identifiable patents in that
country that you have reason to believe are valid.
If, pursuant to or in connection with a single transaction or
arrangement, you convey, or propagate by procuring conveyance of, a
covered work, and grant a patent license to some of the parties
receiving the covered work authorizing them to use, propagate, modify
or convey a specific copy of the covered work, then the patent license
you grant is automatically extended to all recipients of the covered
work and works based on it.
A patent license is "discriminatory" if it does not include within
the scope of its coverage, prohibits the exercise of, or is
conditioned on the non-exercise of one or more of the rights that are
specifically granted under this License. You may not convey a covered
work if you are a party to an arrangement with a third party that is
in the business of distributing software, under which you make payment
to the third party based on the extent of your activity of conveying
the work, and under which the third party grants, to any of the
parties who would receive the covered work from you, a discriminatory
patent license (a) in connection with copies of the covered work
conveyed by you (or copies made from those copies), or (b) primarily
for and in connection with specific products or compilations that
contain the covered work, unless you entered into that arrangement,
or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting
any implied license or other defenses to infringement that may
otherwise be available to you under applicable patent law.
12. No Surrender of Others' Freedom.
If conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot convey a
covered work so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you may
not convey it at all. For example, if you agree to terms that obligate you
to collect a royalty for further conveying from those to whom you convey
the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.
13. Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
combined work, and to convey the resulting work. The terms of this
License will continue to apply to the part which is the covered work,
but the special requirements of the GNU Affero General Public License,
section 13, concerning interaction through a network will apply to the
combination as such.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of
the GNU General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the
Program specifies that a certain numbered version of the GNU General
Public License "or any later version" applies to it, you have the
option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation. If the Program does not specify a version number of the
GNU General Public License, you may choose any version ever published
by the Free Software Foundation.
If the Program specifies that a proxy can decide which future
versions of the GNU General Public License can be used, that proxy's
public statement of acceptance of a version permanently authorizes you
to choose that version for the Program.
Later license versions may give you additional or different
permissions. However, no additional obligations are imposed on any
author or copyright holder as a result of your choosing to follow a
later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
<program> Copyright (C) <year> <name of author>
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<https://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<https://www.gnu.org/licenses/why-not-lgpl.html>.