📖 User Manual

End User Manual

Day-to-day work in the laboratory: orders, samples, results, validation, reports, the surveillance workflows, pathology, NCEs and lab notebooks.

Administrator Guide

Setting OpenELIS up and keeping it running: users, site settings, the test catalog, programs and rules, result reporting and reference data.

End User Quick Reference and Administrator Quick Guide

Short, text-only versions of the common workflows, for when you have done a task once and need a reminder. Older format.

LEGACY Versions

Earlier versions of pages that have been rewritten, and retired screens, kept for sites still on older releases.

📖 Manuel de l’utilisateur

The French manual. It links the pages already translated and points to the English page where there is no translation yet.

Modules & Features

Feature-by-feature reference, such as sample storage, Westgard QC, aliquots and reflex tests.

Navigating OpenELIS Global

Log in and find your way around the Main menu and screens. Older format.

Quick links

Links to commonly used screens. Older format.

Quick troubleshooting

Fixes for common problems, such as required fields that block saving. Older format.

Help

The help and forms available from inside OpenELIS. Older format.

Logging out of OpenELIS

How to log out. Older format.

The three domains and the shared order wizard

How clinical, environmental and vector orders share one four-stage order wizard.

Entering laboratory orders

Search for or add a patient, create an order and print its labels. Older format.

Complete the sample check for an environmental or vector order

Run the acceptance checklist on each sample and release the order for testing. In review.

Electronic orders

Review orders sent to OpenELIS electronically, with their sample and test information. Older format.

Batch order entry

Enter a group of orders that share a sample type, test or facility of origin in one pass. Older format.

Find an existing order

Find an order to view or modify it.

Create aliquots from a sample

Find a sample by accession number and create aliquots (sub-samples) from it.

Track sample storage and disposal

Record where sample items are stored and manage their status and disposal.

Register a new patient

Add a patient record so the patient can be linked to orders. In review.

Patient management

Find an existing patient to view or edit their record. In review.

Merge patient records

Combine two duplicate patient records into one. In review.

Enter a clinical order

Register a clinical order: the patient, the requesting site and provider, and its sample types and tests. In review.

Prepare samples for a clinical order

Record each sample of an order: collection, arrival, labels and storage. In review.

Complete the sample check for a clinical order

Confirm each sample is acceptable and release the order to the laboratory. In review.

Label and store environmental and vector samples

Print order and sample labels and assign storage for environmental and vector orders. In review.

Print a work plan

List the tests waiting in a lab unit, test, panel or priority, and print the work plan. In review.

Enter and save results

Enter results for samples awaiting results and save them so they move on to validation.

Triage and release results

Work through the validation queue, release clear results in one action, and correct or retest the rest. OpenELIS 3.2.2 and later.

Validate and release results

Review entered results and release them, or send them back for retesting. Releases before 3.2.2.

Electronic signatures

Turn on electronic signatures and use them to sign result entry and validation.

Run reports

Generate printable reports and data exports.

Results entry (legacy screen)

The older results entry screen, for sites that still use it.

Custom Data Export and My Report Queue

Build a CSV extract of samples, tests, results and turnaround times without SQL, and rerun it for a new period. In review.

Environmental surveillance workflow overview

The workflow end to end, from sampling-site order to compliance certificate.

Enter an environmental order

Register an environmental sample against a regulatory standard and submit it for testing.

Compliance evaluation

The concepts behind evaluating environmental results against a standard.

Generate a compliance certificate

Produce the compliance certificate for a validated, standard-linked environmental order.

Enter results and read the compliance evaluation

Record results for an environmental order and read the automatic pass or fail verdict. In review.

Validate and release environmental results

Review and release environmental results so they are final. In review.

Vector surveillance workflow overview

The workflow end to end, from order entry through validation.

Enter a vector order

Register a pooled field collection and submit it for testing.

Identify vector species and deconvolute a pool

Identify the species in a pool and deconvolute it.

Record Vector Field Survey indices

Capture larval and pupal survey counts and read the computed entomological indices.

Pooling and deconvolution

The concepts behind pooled testing and deconvolution.

Pathology

Record pathology cases and the examination of tissues, cells and fluids. Older format.

Immunochemistry

Request and record immunohistochemistry tests. Older format.

Cytology

Create, process and finalize cytology requests. Older format.

Report a non-conforming event

Record a quality event such as a damaged or mislabelled sample, link the affected sample and find the event under All NCEs.

EQA provider: run a proficiency testing scheme

Run an EQA scheme for other laboratories: enrol them, ship panels, score results and follow up failures. In review.

EQA participant: take part in a proficiency testing scheme

Enrol in an EQA scheme, test the panel, submit results and act on the scores. In review.

Statistical QC: overview and daily review

Find statistical QC in OpenELIS and check each day whether any control has failed. In review.

Receive and activate a control lot

Register a new lot of control material so its results are judged against the lot's targets. In review.

Review and act on alerts

See the alerts OpenELIS has raised, such as overdue STAT orders and EQA deadlines, and record what was done. In review.

Test accreditation and report logos

Record the bodies that accredit your laboratory and their tests, so reports carry the right logo. In review.

Laboratory notebooks

The entry page for the notebook workflows. Older format.

How to create a lab notebook

Set up a project notebook, then work samples through its stages from processing to archiving, one how-to page per stage. Older format.

Introduction

What the administrator guide covers. Older format.

Accessing the administration module

Open the Admin area from the Main menu. Older format.

Navigating OpenELIS LIMS

The main screens and menus, from an administrator’s point of view. Older format.

Manage user accounts

Create user accounts and set each user’s roles and permissions.

Manage organizations

Register the referring clinics, referral labs, health districts, sampling sites and vendors OpenELIS works with. In review.

Manage providers

Register the clinicians who order tests, so they can be chosen on an order.

Import and export locations

Load or update organizations, wards, sampling sites and geographic areas in bulk from CSV files. In review.

Manage geographic areas

Keep the list of administrative areas that patient addresses, organizations and sampling sites point to. In review.

Manage sampling sites

Record the fixed places where environmental samples are collected. In review.

Configure site information

Set the properties that identify your laboratory and control site-wide behaviour.

General Configurations reference

Look up what each setting under Admin → General Configurations does: order entry, result entry, patient entry, validation, non-conformity, work plan and printed report settings.

Choose the lab number format

Choose how lab (accession) numbers are generated for new orders.

Edit application properties

Set the system-wide properties for facility identity, integrations, notifications and paging.

Manage non-working days

Set the holidays and weekend days excluded from turnaround time.

Configure logging

Change the logging level at runtime and watch the live application log.

Rebuild the search index

Rebuild the index behind global search.

Configure the navigation menu

Choose which entries appear in the Main menu, and how each one is shown.

Test catalog workflow overview

The test catalog pages, in the order you usually configure a test.

Add a test to the test catalogue

Define a new test so it can be ordered and resulted.

Add a sample type

Define a new specimen type so tests can be configured and samples collected for it.

Add a lab unit

Define a laboratory unit so tests can be assigned and orders routed to it.

Create a test panel

Bundle several tests so they can be ordered together.

Find and filter tests in the catalog

Locate a test in the catalog and open it for editing.

Edit a test’s Basic Info

Set a test’s domain, AMR surveillance flag and status.

Configure sample types and result components

Define how a test’s results are captured: components, type and unit.

Set reference and critical ranges

Define normal and critical ranges and check demographic coverage.

Link methods to a test

Associate testing methods with a test.

Map a test to terminology codes

Map a test to LOINC, SNOMED, CIEL or OCL codes.

Add a test to panels

Include a test in one or more panels and set its position.

Set test display order within a sample type

Control the order tests appear in for a sample type.

Configure sample storage and disposal

Record storage conditions, stability and disposal for a test’s samples.

Manage label presets

Create or edit a reusable barcode label definition.

Sample Acceptance Checklist

Define the acceptance criteria staff confirm, per domain, and how strictly they are enforced.

The unified test editor

How the Test Catalogue Management editor is laid out and how its sections save. In review.

Duplicate a test

Start a new test from a copy of an existing one. In review.

Read-only and cross-link sections

The editor sections that show information kept elsewhere, and where to change it. In review.

Manage lab units

Create and maintain lab units: their domain, whether they are active, their tests and their display order. In review.

Import a test catalog from CSV

Load or update the test catalog from CSV files instead of editing tests one at a time. In review.

Author the test catalog in CSV files

Write the CSV files a site's test catalog is loaded from. In review.

Define programs and their questionnaires

Set up the programs orders are filed under, and the extra questions reception answers for them.

Manage dictionary entries

Manage the coded value lists OpenELIS uses, such as result value options.

Define reflex testing rules

Add a follow-up test or note automatically when a result meets a condition.

Define calculated value tests

Compute a test’s result automatically from other results, values or patient attributes.

Configure test notifications

Choose which notifications are sent for each test, to patient or provider, by email or SMS.

Configure result reporting to external systems

Set the external endpoints OpenELIS sends results and surveillance reports to.

Analyzer management

Configure laboratory analyzers, set up field mappings and monitor results coming in. Older format.

Set up an analyzer