Methods IFU031(04)

What is a Method?

A Method defines how the RARE platform should capture, process, and interpret images for a specific test on a given Housing. It brings together:

• The physical test format – via the selected Housing

• The camera and optics setup – via Camera Optics

• The reader behaviour – via Reader Configuration and Reader Parameters

• The strip‑level regions and corrections – via Configure Strips

In practice, a Method tells the RARE system:

• Which Housing and Camera Optics to use when capturing images

• How the reader should behave during capture (e.g. Flash, Data collection mode, number of Frames to capture)

• Which parts of each strip to analyse:

  • The ROI (corners) for each strip

  • The profile regions where Control and Test lines are expected

• How to apply control‑based corrections:

  • Whether to use Control Exposure, Control line correction and Control baseline

  • How far to extend or trim the control region

  • How to search for the control line (e.g. Div profile, Step search, Search Min/Max, Minimum Fit percentage, Search Method)

  • How to model and correct the baseline (e.g. Polynomial baseline order, Initial H Scale factor, Control baseline threshold)

Together, these settings determine how raw images from the camera are turned into stable, reliable line profiles that can then be interpreted as qualitative or quantitative results.

Methods are created and maintained by paid users using the Create Method workflow and are then used downstream alongside Batches, Classifiers, and Ground Truth data to generate diagnostic outputs.

Method Management

Accessing

1. Log in to the RARE Portal as a paid user.

2. In the left-hand sidebar, go to Configurations → Methods (or Method Management, depending on your build).

3. The Method Management page opens, showing a list of all existing Methods that have been configured for your environment.

Understanding the Method Management list

The Method Management list gives you a table of all previously saved Methods.

Each row represents a single Method configuration. By default, the list typically includes columns such as:

• ID – System-generated unique identifier for the Method.

• Method Name – Human-readable name (e.g. “CRP Quantitative v2”).

• Description – Short description (e.g. target analyte, assay type, customer, or use case).

• Organisation - Associated organisation name who owns the Method

• Version - the version of the Method, tracking edits

• Status – Whether the Method is currently Active, Inactive, In Progress, or For Datarun.

• Date Created – When this Method configuration was first created.

• Date Updated – When it was last changed.

• Actions – Menu or buttons to view, edit, enable/disable, or create a Method.

Use this list to quickly see:

• Which Methods are available for use

• Which Housing each Method is built on

• Whether a Method is active or has been disabled

• When each Method was last updated

Filtering and sorting Methods

To help you find the right Method quickly, you can:

Filter

At the top of the table, use the filters to narrow down the list, for example by:

• Method Name or ID – Start typing to match specific Methods.

• Organisation – Filter Methods linked to a particular Organisation.

• Status – Show only Enabled or Disabled Methods.

• Date range – Limit to Methods created or updated within a specific period.

Sort

Click on a column header (such as Updated date, Name, or Housing) to sort the list in ascending or descending order. This is useful to:

• Bring the most recently updated Methods to the top

• Group Methods alphabetically by name

• Group Enabled / Disabled Methods together

Actions available for each Method

Each row has an Actions menu (e.g. a “…” menu or a button group). Depending on your implementation, this typically includes:

• Edit / View – Open the Method in edit mode (see “Viewing and Editing an Existing Method” below).

• Enable / Disable Method – Toggle whether this Method can be used with Batches / products.

• Create New Method – This is available from the list header.

Use these actions to manage your catalogue of Methods without leaving the main list view.

Creating a New Method

You can create a new Method from the Method Management list.

1. From the Method Management page, click Create New Method.

2. The Create Method workflow opens with the following steps:

   1. Describe Method

   2. Housing & Camera Optics

   3. Configure Reader

   4. Load Test Image

   5. Configure Strips

   6. Save

Step 1 – Describe Method

On the first screen you define the basic identity of the Method.

• Method Name (required)

  • What it is: The primary name shown in the Methods list and anywhere this Method is referenced.

  • Guidance:

    • Include analyte, qualitative/quantitative, and version where relevant.

    • Examples:

      • CRP Quantitative (mg/L)

      • COVID‑19 Ag Qualitative.

• Method Description

  • What it is: A short explanation of what this Method is for.

  • Guidance:

    • Mention the assay type, sample type, and intended use.

    • Example: Semi‑quantitative CRP assay for serum samples, 5–200 mg/L.

Step 2 – Housing & Camera Optics

In this step you link the Method to its physical Housing and define which camera optics configuration will be used.

• Select Housing (required)

  • What it is: The Housing that defines the physical layout (strips, windows, lines) for this Method.

  • Behaviour:

    • Only Housings that have been created (and typically Enabled) in Housings configuration will appear.

  • Guidance:

    • Choose the Housing that matches the actual test device used for this Method.

    • If you don’t see the expected Housing, check the Housings page.

• Select Camera Optics (required)

  • What it is: The camera/optics configuration used when capturing images for this Method (for example device-specific lens/lighting settings).

  • Guidance:

    • Select the optics profile that matches the device or camera system your users will run this Method on.

    • Use the same optics setting that was used during development/validation.

Step 3 – Configure Reader

This step defines how the reader collects image data and applies global processing before looking at individual strips.

Reader Configuration - Data collection mode ON

Enables additional data capture (e.g. saving extra frames or debug data) when the Method runs.

Reader Parameters are minimal, controlling the flash and number of frames only. Default values are shown where applicable.

Reader Configuration - Data collection mode (OFF)

Disables additional data capture when the Method runs, for routine production use to minimise data volume while representing the operation of a production app.

Reader Parameters control the behaviour of the camera and the initial signal processing. Default values are shown where applicable.

Step 4 - Load Test Image

In this step you load a representative test image that will be used to define the strip regions and line positions in the next step.

Choosing a suitable image

When selecting an image to use in this step:

• The image must have been captured using:

  • The same Housing you selected in Step 2, and

  • The same Camera Optics configuration you selected in Step 2.

• The assay on the strip should be fully developed, with:

  • A clearly visible Control line, and

  • All Test line(s) you intend to configure present and visible.

• The strip should be positioned in the image in a typical, well‑aligned way (not at an extreme angle or off‑centre).

Select image

1. On the Load Test Image step, click Select Image.

2. Select an existing result derived from the selected Housing
   

   

   
   

3. Select an image from the available list/gallery of frames from the result.
   

   

   
   

4. Confirm your selection to load the image, ready to configure strip ROIs and line positions.

Step 5 – Configure Strips

Here you define the regions of interest on each strip and how the control line correction should behave.

If the selected Housing contains multiple strips, you will configure each strip in turn. For each strip:

Select corners (for ROI)

In this part you are telling the system where the strip sits in the image.

1. Look at the loaded test image and, for the current strip, click on three of its four corners.

2. As soon as you have clicked three corners, the system will automatically calculate the fourth corner representing a rectangle around the strip.

3. This bounding rectangle is the Region of Interest (ROI). Everything inside it will be used when the strip is analysed; everything outside is ignored.
   

You can also control which way along the strip the profile is taken (for example, left‑to‑right or bottom‑to‑top) using the on‑screen directional arrows. Set this so that the profile direction follows the normal flow of the assay (from sample pad towards the distal end).

Aim for the ROI to comfortably cover the full length and width of the strip, including all lines, without too much empty background.

Set profile regions

Once the strip’s rectangle and direction are set, the system generates an intensity profile along the strip and displays it beneath or alongside the image. This profile is a graph showing how signal intensity changes along the length of the strip.

The next step is to tell the system where on that profile the lines and baseline live:

1. Position the line regions

   Use the on‑screen tools to place the profile regions over the parts of the profile where the Control and Test lines appear.

   • Each region should sit over a visible peak in the intensity profile that corresponds to a real line on the strip.

   • For example, place one region over the Control line peak, and one (or more) over the Test line peak(s).

   These regions tell the reader: “look here for the Control line” and “look here for the Test line(s)”.

2. Set the baseline regions

   Next, define the baseline regions — parts of the profile where no lines are expected and the signal should represent background.

   • Place these regions in flat sections of the profile, away from any peaks.

   • The baseline is used to measure background intensity so that line signals can be corrected or normalised against it.

3. Visually check alignment

   • Confirm that each Control/Test region lines up both with:

     • The lines in the image, and

     • The corresponding peaks in the intensity profile.

   • Confirm that each baseline region sits over background areas (flat profile segments where no lines are present).

If your test image has all lines clearly visible (as recommended in Step 4), the profile regions should sit neatly over the peaks for each line, with baseline regions in the “flat” parts between or around them.

Control Line corrections

These parameters fine‑tune how the system uses the control line region to correct or interpret signals.

Repeat the configuration for each strip defined by the selected Housing.

Step 6 – Save

The final step lets you review your configuration and save the Method.

Review

• Check the summary of:

  • Method Name and Description

  • Selected Housing and Camera Optics

  • Reader Configuration and Reader Parameters

  • Strip configurations and control‑line correction settings

Save options

• Click Save (or Create Method) to create the Method.

• The new Method will appear in the Method Management list. Its status/availability will follow whatever default behaviour your system uses for newly created Methods (for example, Enabled or Disabled by default).

When to change defaults (and when not to)

Most of the parameters in Configure Reader and Configure Strips are low‑level image‑processing controls.

In general:

• If you are setting up a new Method based on an existing, validated one, start from the same values and only change:

  • Method Name

  • Method Description

  • Housing / Camera Optics (if the physical device or capture device differs)

• Only adjust items like Frames to capture, Polynomial baseline order, Minimum Fit percentage, Search Max, etc. if:

  • You are actively tuning performance with test data, and

  • You have agreement within your dev/validation team on the new setting.

If you are unsure about a parameter:

• Prefer the default value shown in the UI.

• Capture a note (e.g. in your validation log or change log) whenever you deliberately diverge from the defaults.

Viewing and Editing an Existing Method

Open an existing Method

1. From the Method Management list, locate the Method you want to update.

2. In the Actions column, choose View.

3. The Method Detail page opens, showing (for example):

   • Method Name and Description

   • Method ID

   • Linked Housing

   • Result type / mode and any classifier configuration

   • Configured measurement regions / lines

   • Current Status (Enabled / Disabled)

   • Created and Last updated information

Making changes

1. Update any of the editable fields, for example:

   • Refining the Description to better describe the assay

   • Adjusting the interpretation rules (e.g. cut-offs, thresholds, or mapping logic)

   • Changing region configuration if the Method should use different lines or windows on the Housing

2. If permitted, toggle the Status between Enabled and Disabled.

3. When finished, click Save Changes and a new version will be created.

You are returned to the Method Management list, and the Updated date reflects your latest changes.

Enabling or Disabling a Method

As a paid user, you can control whether a Method can be used in active workflows.

1. From the Method Management list, locate the Method.

2. In the Actions menu, choose Enable Method or Disable Method.

3. Confirm the change if a confirmation dialog appears.

Typical behaviour:

• Enabled Methods can be selected when configuring Batches / products and used during testing.

• Disabled Methods remain in the list (for traceability) but are not available for new Batch configurations or active use.

Permissions and visibility

• Paid users

  • Can access Method Management from the sidebar.

  • Can create, view, edit, enable, disable, and (where available) duplicate Methods.

• Non-paid or restricted users

  • May not see Method Management in the sidebar, depending on your configuration.

  • Interact with Methods indirectly via configured Batches, tests, and results.

This ensures that any authorised paid user can configure and maintain Methods, while access for other users can be limited to running tests and viewing results.