Getting Started with ClinicFlow

A step-by-step guide to setting up and running your first payroll

1. Create Account
2. Configure Settings
3. Export from Jane
4. Generate Payroll
5. Review Workbook
6. Send Invoices
7. Track Approvals
Step 1 Create Your Account
  1. Go to the ClinicFlow home page and click Get Started or Start Free Trial.
  2. Enter your name, email address, and choose a password (minimum 8 characters).
  3. Pilot / invite code — if you received a pilot code from iMentalHealth, enter it in the Invite Code field. This gives you a 2-month free trial with full access.
  4. Click Create Account. You'll land on Settings to complete your setup.
No credit card is required to create an account. Pilot users get 60 days free. After your trial, subscribe on the Pricing page.
Subscription options
  • Monthly — $59 CAD/month
  • Annual — $549 CAD/year (save $159)
  • Up to 30 contractors, unlimited payroll runs
Step 2 Configure Your Settings

Settings are shared across every payroll run. Fill these in once — ClinicFlow will pre-fill every workbook for you.

A. Clinic Identity
  • Clinic Name — appears on all invoices
  • Address — full mailing address
  • GST / HST Number — e.g. 123456789 RT0001
  • Fiscal Year — e.g. 2026
B. Contractor Rate Card

Up to 30 contractors. For each one:

  • Name + Email — used for invoice delivery
  • GST # — contractor's business number
  • T1 Rate — therapy payout % for sessions 1–threshold (e.g. 60 for 60%)
  • Threshold — session count where T2 rate kicks in
  • T2 Rate — payout % after threshold
  • Report / Court / VAC / Supervision — payout % per service type
Enter rates as whole numbers: 60 means 60%, not 0.60.
C. Service Type Mappings

Maps each Jane service name to a ClinicFlow billing category. Common ones are pre-loaded. Add any custom services from your Jane account.

Default categories:
  • Therapy
  • Report / Assessment
  • Court Report
  • VAC Therapy
  • VAC Assessment
  • Supervision
  • No Charge
Complete Settings before generating any payroll. Contractor names and rates are embedded in the downloaded workbook — changes in Settings only apply to future runs.
Step 3 Export Your Jane Invoice Report
In Jane, follow these steps:
  1. From the top menu, click Schedule.
  2. Click Reports in the left sidebar.
  3. Select Invoices.
  4. Set the date range to cover the full payroll month (e.g., March 1 – March 31, 2026).
  5. Apply any filters needed (location, staff member).
  6. Click Export CSV.
  7. Open the downloaded .csv file in Excel or a text editor.
  8. Press Ctrl+A to select all, then Ctrl+C to copy.
Note: If you open the CSV in Excel first, make sure to copy from the CSV view (not a formatted table) to preserve the raw comma-separated format that ClinicFlow expects. Alternatively, open the file in Notepad and copy from there.
Required CSV columns

ClinicFlow expects these exact column headers in your Jane export:

Location
Purchase Date
Invoice Date
Patient
Item
Staff Member
Payer
Invoice #
Status
Subtotal
GST
Total
Collected
Balance
Standard Jane invoice export includes all of these by default.
Step 4 Generate Your Payroll Workbook
  1. Click Generate Payroll in the top navigation.
  2. Select the Payroll Month from the dropdown (e.g., March).
  3. Confirm or adjust the Fiscal Year.
  4. Paste your copied Jane CSV data into the text area.
  5. Click Generate Workbook & Download.
  6. Your browser will download a file named ClinicFlow_[ClinicName]_[Month].xlsx.
No CSV yet? Leave the text area blank and click Generate. You'll get a fully structured workbook with all your clinic settings pre-filled — you can paste data manually into the Raw Data tab in Excel.
You can generate the workbook multiple times for the same month — each run creates a fresh, clean file. Previous runs are logged in your Dashboard.
Step 5 Review Your Workbook

Your downloaded Excel file contains 10 tabs. Here's what each one does:

Tab Purpose What to do
Cover / Instructions Overview of the workbook, contact info, and tab guide. Read only
⚙ Settings Clinic details, contractor rate card, and service type mapping — pre-filled from your portal settings. Review; yellow cells are editable
📋 Raw Data Every invoice row from your Jane CSV, with date, patient, item, payer, and amounts. Review; add/remove rows if needed
🚦 Payment Status Auto-flags each invoice as Paid, Partial, or Unpaid based on Balance column. Review only — formula-driven
📊 Contractor Summary Per-contractor payroll: T1/T2 therapy, reports, court, VAC, supervision — auto-calculated from Raw Data. Review payouts; confirm against Jane
🧾 Invoices Printable invoice for each contractor showing session counts, gross, rate, and payout. Print or save; invoice #s editable
🏦 Clinic Revenue Total gross revenue by payer (Blue Cross, Medavie, WCB, VAC, Private) and by service type. Review monthly revenue breakdown
📈 P&L Dashboard 12-month P&L: gross revenue, contractor payouts, net. Auto-fills current month. Archive each month with Paste Special → Values
⚠ Unpaid Clients List of all client invoices with outstanding balances for follow-up. Follow up on collections
📬 Invoice Status Tracks which contractors have been emailed and whether they have approved. Updated by the portal when you send invoices
Yellow cells are editable input fields — everything else is formula-driven. Do not paste values over formula cells or the workbook calculations will break. To archive a month's P&L data: copy the row → Paste Special → Values Only.
Step 6 Send PDF Invoices to Contractors
  1. Click Invoices in the top navigation.
  2. Find your payroll run in the list and click Send Invoices.
  3. ClinicFlow generates a PDF invoice for each contractor and emails it automatically.
  4. Each email includes:
    • The contractor's PDF invoice as an attachment
    • A unique one-click approval link
    • Clinic name, invoice number, and payroll month
Invoices are sent to the email addresses entered in Settings → Contractor Rate Card. Double-check contractor emails before sending.
What the contractor receives
  • An email from your clinic's address
  • Subject: "[ClinicName] Invoice — [Month] [Year]"
  • PDF attachment with session breakdown and payout amount
  • A button: "Review & Approve Invoice"
Step 7 Track Contractor Approvals
For the contractor:
  1. They receive the invoice email.
  2. They click the Review & Approve Invoice link.
  3. They review their invoice in the browser.
  4. They click Approve — done.
For the clinic admin (you):
  • Go to Invoices in the portal.
  • See each contractor's status: Sent, Approved, or Not Sent.
  • The Invoice Status tab in your Excel workbook also reflects these statuses.
  • No chasing contractors by email for signatures.
Managing Your Subscription

After your trial period, subscribe on the Pricing page. You can update your payment method, download receipts, or cancel anytime via the Billing link in the top navigation (powered by Stripe — no card details are stored by ClinicFlow).

TROUBLESHOOTING
My contractor payouts are $0 — what happened?

Check that the Staff Member names in your Jane CSV exactly match the contractor names in Settings. ClinicFlow matches on name — even a trailing space or different capitalisation will cause a mismatch. Copy the name directly from Jane.

A service type is showing as Uncategorised.

Go to Settings → Service Type Mappings and add the Jane service name exactly as it appears in your CSV (copy-paste from the Item column to be safe). Assign it to the correct category and save.

The workbook downloaded but some numbers look wrong.

Re-check your Settings: confirm Tier 1 % and threshold are correct for each contractor, and that the fiscal year matches. Regenerate the workbook after saving any changes.

Contractors are not receiving invoice emails.

Confirm contractor email addresses are correct in Settings. Check your spam folder. If you are testing locally, SMTP must be configured in your .env file. Contact support if the issue persists.

I need more than 30 contractors.

Contact us at admin@imentalhealth.ca — we can accommodate even larger clinics.

Does ClinicFlow work with Jane?

ClinicFlow is designed to work with the invoice CSV export from Jane (jane.app). It is an independent tool and is not affiliated with or endorsed by Jane. If your scheduling system can export the same column structure, it will also work. Contact us for help mapping your export.

Ready to run your first payroll?

Create your account and configure settings in under 10 minutes.

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