Western Blot Utility: Streamlining Blot Analysis with Precision and Efficiency

Experience the next generation of western blot analysis with our comprehensive software solution.

Western Blot Utility is a modern desktop application built to streamline the organization, quantification, and analysis of western blot experiments. Designed with a focus on data integrity, transparency, and privacy, it empowers researchers to produce consistent, auditable, and reproducible results—without relying on manual macros or third-party plugins.

All data remains private and is stored locally on your machine—never sent to the cloud—giving you full control over sensitive research data.

Key Features

NOTE We are about to get an exciting ugrade with v1.0.0 to our automated band detection as we transition to using AI rather than a hueristic algorithm.

End-to-End Experiment Management: Seamlessly group and analyze multiple images within a single experiment, ensuring consistent and reproducible results.
Automated Band Detection: Utilize advanced algorithms to automatically identify and quantify bands, significantly reducing manual intervention and potential errors.
Comprehensive Normalization: Achieve accurate normalization across your dataset, facilitating reliable comparisons and robust data interpretation.
Integrated Audit Capabilities: Maintain full transparency with built-in audit logs, enabling traceability and verification of all analytical steps.
User-Friendly Interface: Navigate effortlessly through your data with intuitive controls, including save states, undo/redo functionality, and efficient image navigation.

Who Is This For?

The Western Blot Utility is ideal for researchers who:

Process large volumes of western blot images
Need consistent and automated normalization of blot data
Value reproducibility, transparency, and auditability in their workflow
Are frustrated with fragmented workflows in tools like ImageJ, Image Studio, or Photoshop
Want basic usability functionality like undo and redo that are frequently missing in scientific tools

Accuracy You Can Trust

All measurements are taken directly from the raw image—no compression, no scaling.
Calculations are based on peer-reviewed methods, tested with a comprehensive suite of automated and manual validations.
Built in collaboration with a third-party researchers (Harvard-affiliated) to ensure independent validation.
Complete transparency: review our audit documentation for full traceability.

If you ever find a discrepancy, we encourage you to file a bug — transparency and scientific integrity are core to what we do.

Get Started Today

Ready to jump in? Visit the Installation page to download Western Blot Utility and start your analysis with our free trial today.

We Value Your Feedback

We're committed to continuous improvement. If you have suggestions, issues, or ideas for features that would better support your work, send us your feedback. Your input helps shape a better tool for the research community.

Sponsorship

If you like what we do, consider supporting us. gh/blackberryfloat @ thanks.dev

Installation

The Western Blot Utility is a licensed desktop application. We have prebuilt tested binaries for x86_64 architectures running Windows or Linux operating systems that you can download below. If you need a custom build, reach out to blackberryfloat+wbu@gmail.com.

Licensing

While the Western Blot Utility is a licensed application, licenses are FREE. For all licensing requests, please reach out to blackberryfloat+wbu@gmail.com. Please use the email address you want the license associated with when reaching out. Currently, we only allow one device per user, with exceptions being handled on a case-by-case basis.

NOTE To be transparent, we need to fund development so we can best support you. Thus, our goal is to always give you the option of either a free version with minimal Ads or a paid license. To support this we must reach a critical mass of users so that advertisers are interested in this platform. The free licenses are the best way to track this information.

Install Western Blot Utility on Windows

Download the executable linked below by clicking the button. This binary is a .exe file, so your device might flag it as untrusted and require your permission to run. This is expected.

{WINDOWS_X86_64_EXE}

Once downloaded, you can double-click the file to run the application, and that is it! Happy analyzing!

Install Western Blot Utility on Linux

Download the executable linked below by clicking the button. This binary is an executable file, so your device might flag it as untrusted and require your permission to run. This is expected.

{LINUX_X86_64}

Once downloaded, mark the file as executable as noted below, and then you can double-click the file to run the application, and that is it! Happy analyzing!

NOTE You might have to mark the file as executable before you can double click it to run. You can do this by right clicking on the file in the folder explorer, click the properties option, and toggle the "Executable as program" button to "on". You can also open the file in the terminal and use the chmod +x <filename> command.

Install Western Blot Utility on Mac

We currently support executable files for Macs with either Apple Silicon or Intel chips. Download the file by clicking the relevant button below. Mac will most likely flag the executable as untrusted since it is not being delivered through the App Store. This is expected.

{MAC_APPLE_SILICON_X86_64}

{MAC_INTEL_X86_64}

Once downloaded, you have to mark the file as executable. You do this by opening a terminal, navigating to your downloads and then use the chmod +x <filename> command. Now in finder you can double click the file to run it. If this is the first time, your Mac will complain the file is untrusted. You must follow the instructions documented here to resolve this.

User Guide

Lets get started! In this chapter we will learn the basics about how to use the Western Blot Utility to process your experiment.

Western Blot Utility Key Terminology

Name	Description
Experiment	A project that investigates the effects of various compounds and doses on substances to assess the viability of a compound for drug use. In this application, an experiment is represented by a folder on the file system, typically containing images.
Image	A digital scan of an optimally exposed blot stained with a specific antibody.
Lane	Represents a single case containing a unique set of independent variables, such as drug type, dose, and time factor.
Region of Interest (ROI)	A specific rectangular area of pixels within an image and lane that represents the effectiveness of a case. Intensity calculations are performed based on this region.

Opening a Western Blot Experiment

The process for opening an experiment or creating a new one is the same:

Open the file menu.
Click Open.
Select a folder containing the images you want to process.

NOTE
A file with the .wbu extension will be created in the selected folder. This file contains the application state information for that experiment. It is a JSON object, meaning it is human-readable if you want to inspect it. However, it is strongly recommended that you do NOT modify it, as this could cause issues when the application is loaded next time.

Quantifying a Western Blot Image

NOTE
This assumes you have already opened the experiment as outlined in Opening an Experiment.

To quantify an image, select the relevant image in the explorer panel on the left. Images are listed under the Data collapsible header. Selecting an image will open it for annotation.

Reference Region of Interest Extrapolation

Currently, the application supports one proprietary quantification method called Reference ROI Extrapolation.

NOTE
This is a heuristic algorithm designed to assist users, not automate the process. It may not always provide an ideal solution. It works best with clean images that are not skewed and have a clear distinction between background and foreground.

To use this method, start by drawing a rectangle around the relevant ROI on the far left. This is done via a click-and-drag process. When you release the mouse, the rectangle will be finalized, and all other ROIs will be automatically estimated. At this point, you can resize, move, add, or delete ROIs as needed. You can also restart the process using the undo pathway, the Clear ROIs button, or the Clear Lanes button. The right-side panel provides a quick snapshot of intensity values per lane/ROI and allows you to label controls.

NOTE
Tight reference ROIs tend to yield the best results.

Resize a Region of Interest

All resize operations apply globally to all ROIs. Currently, the application does not support independently resizing individual ROIs. At the top of the right-side panel, you will find widgets for modifying the width and height of ROIs.

Move (Translate) a Region of Interest

To move an ROI, click and hold inside the ROI, then drag it to the desired position. For fine control over a specific ROI, hover over it to view the lane ID. In the right-side panel, you can use the fields under the associated lane header to adjust the x and y pixel positions of the ROI's top-left corner.

Add a Region of Interest

You can add an ROI at any time by clicking on the image. A new rectangle will be created at the cursor's position.

Delete a Lane and/or Region of Interest

To delete an ROI, right-click on it to open the context menu, then select Delete. Alternatively, you can use the Del button, but this will only remove the last ROI. If you need to restart, use the Clear ROIs button at the top of the right-side panel.

It is important to note that deleting an ROI is not the same as deleting a lane. To delete a lane, click the Clear Lanes button in the right-side panel or right-click the lane name in the side panel, then select Remove Lane from the context menu. Lanes and ROIs are handled separately so that lane metadata can be preserved as you manage ROIs. When ROIs are edited (except for deletion), they are automatically remapped to lanes to ensure the order of ROIs matches the order of lanes.

WARNING
The independent control of ROIs and lanes is intentional but can lead to confusing behavior if not handled carefully. The most common issue is extra lanes with no associated ROIs. This can cause loading controls to be ignored, as they won't match the target lane count. To resolve this, remove the extra lanes when this occurs.

Audit the Quantification Results for a Blot Image

Producing accurate results is our top priority. All data measurements are taken directly from the raw image without any scaling. Calculations are based on published methods and are supported by an extensive suite of automated test cases, along with manual verification by beta users. However, mistakes can happen, so we provide the audit functionality to empower you to double-check our work if needed.

This feature allows you to export a per-image CSV file, giving you full transparency into the calculations performed for each ROI behind the scenes. It provides complete access to the raw values, enabling you to reproduce the calculations manually if desired.

Open the file menu.
Click Audit Image.
Select an output location for the CSV file.

If you find any issues with the integrity of our data, please file a bug immediately.

Export Quantification Data

This application allows you to export the calculated intensities for your experiment to a CSV file. You can choose from three export methods: summed, average, and normalized.

Summed is recommended if you have no controls.
Normalized is recommended if you have labeled your controls. The normalized value is calculated if you provide any combination of a loading control, internal control, or both.

If no controls are provided, the export will result in an empty CSV file.

Open the file menu.
Click Export.
Select the desired export method (e.g., normalized).
Choose an output location in the file dialog.

Community

Community feedback and engagement is welcome, encouraged in fact!

Submit Feedback

We always want to know what we can do to make our product better. You are our best resource. You can submit feedback by filling out this form here.

If the feedback is about how to improve the product, use the new feature template.

If the product is behaving in a way that contradicts the documentation or seems to like it is behaving in a way that was not designed, use the new bug template.

Western Blot Utility Docs