# Omni-stainer user guide

## Omni-stainer user guide

- [Overview](https://docs.parheliabio.com/overview.md): Parhelia Omni-Stainer™ system is a precise, cost-effective tissue stainer designed to deliver consistent results while offering substantial savings in reagents and time.
- [Quick Start: Omni-Stainer™ Bundles](https://docs.parheliabio.com/product-guides/quick-start-omni-stainer-tm-bundles.md): Manual and Automated Set Up
- [Omni-Stainer™ Box Contents](https://docs.parheliabio.com/product-guides/omni-stainer-tm-box-contents.md): First, let's get acquainted with the Box Contents.
- [Additional materials](https://docs.parheliabio.com/product-guides/additional-materials.md): These consumables are required in addition to a Parhelia Omni-Stainer™ Automation Bundle for the first runs
- [S12 Assembly and Sample Prep](https://docs.parheliabio.com/product-guides/s12-assembly-and-sample-prep.md): How to put together your Omni-Stainer™ S12 system and prepare samples for staining
- [C12 Assembly and Sample Prep](https://docs.parheliabio.com/product-guides/c12-assembly-and-sample-prep.md): How to put together your Omni-Stainer™ C12 system and prepare samples for staining
- [Sample Mounting Instructions](https://docs.parheliabio.com/product-guides/sample-mounting-instructions.md): To ensure bubble-free operation, use these directions for S-type and C-type flow cell construction / sample mounting.
- [Manual Operation and "Blue Dye Demo" Manual Protocol](https://docs.parheliabio.com/product-guides/manual-operation-and-blue-dye-demo-manual-protocol.md): The Manual Product Bundles and the Automated Product Bundles can both be operated manually with a P200 micropipette.
- [Automation (Opentrons OT-2) Setup](https://docs.parheliabio.com/product-guides/automation-opentrons-ot-2-setup.md): This page goes through setting up a new Opentrons OT-2, most of the content is in links to Opentrons website and Opentrons videos.
- [Omni-Stainer Automation Overview](https://docs.parheliabio.com/product-guides/automation-opentrons-ot-2-setup/omni-stainer-automation-overview.md): Roadmap for Getting Set up with the Omni-Stainer in an Opentrons OT-2
- [Importing labware definitions](https://docs.parheliabio.com/product-guides/automation-opentrons-ot-2-setup/importing-labware-definitions.md): Custom labware definitions have been meticulously created for Parhelia Omni-stainer instruments and reservoirs, these files are essential for running Parhelia Bio protocols.
- [Opentrons App v7 Updated Labware Definitions](https://docs.parheliabio.com/product-guides/automation-opentrons-ot-2-setup/importing-labware-definitions/opentrons-app-v7-updated-labware-definitions.md): If running Opentrons app v7.0 or above, the "v7" version of the labware should be used to avoid automation errors.
- [StainWorks](https://docs.parheliabio.com/product-guides/automation-opentrons-ot-2-setup/stainworks.md): StainWorks allows for simple no-code customization of staining protocols.
- [Labware Layouts](https://docs.parheliabio.com/product-guides/automation-opentrons-ot-2-setup/labware-layouts.md): Labware Layout files are .xlsx files that differ in complexity depending on the complexity of the staining protocol.
- [Thermal Sheath & Temperature-controlled incubations](https://docs.parheliabio.com/product-guides/automation-opentrons-ot-2-setup/thermal-sheath-and-temperature-controlled-incubations.md): This page is under construction, please reach out to our team for help with the thermal sheath and temperature modules.
- ["Blue Dye Demo"  Automated Protocol](https://docs.parheliabio.com/product-guides/blue-dye-demo-automated-protocol.md): This demo protocol demonstrates the basics of automated capillary gap staining liquid exchange with an C12/S12 Omni-Stainer™
- [Software Requirements](https://docs.parheliabio.com/product-guides/software-requirements.md)
- [PhenoCycler® (CODEX)](https://docs.parheliabio.com/protocol-knowledge-base/phenocycler-r-codex.md): PhenoCycler Fusion (PCF) and IHC were the first applications of Parhelia's capillary gap staining automation, so there is a great background of knowledge and support for this particular application.
- [Gram Stain](https://docs.parheliabio.com/protocol-knowledge-base/gram-stain.md): This page is under construction
- [IF](https://docs.parheliabio.com/protocol-knowledge-base/if.md): This page is under construction
- [IHC](https://docs.parheliabio.com/protocol-knowledge-base/ihc.md): This page is under construction
- [H\&E](https://docs.parheliabio.com/protocol-knowledge-base/h-and-e.md): This page is under construction
- [RNAScope](https://docs.parheliabio.com/protocol-knowledge-base/rnascope.md): This page is under construction
- [Opal](https://docs.parheliabio.com/protocol-knowledge-base/opal.md): This page is under construction
- [IMC](https://docs.parheliabio.com/protocol-knowledge-base/imc.md): This page is under construction
- [Background info and Lens training docs](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs.md): This section of the Gitbook is primarily for training the Lens AI search tool, and is not really crafted for human absorption. Please follow the Product guides rather than this section.
- [Importing labware definitions](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/importing-labware-definitions.md): Custom labware definitions have been meticulously created for Parhelia Omni-stainer instruments and reservoirs, these files are essential for running Parhelia Bio protocols.
- [StainWorks software: a centralized app for accessing and configuring protocols](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/stainworks-software-a-centralized-app-for-accessing-and-configuring-protocols.md)
- [Reagent Layout files](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/reagent-layout-files.md)
- [Running the "Blue Dye Demo" protocol](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/running-the-blue-dye-demo-protocol.md)
- [Copy of CODEX (PhenoCyler™)](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/copy-of-codex-phenocyler-tm.md): Omni-Stainer + OT-2 automates the entire 5.5 hr (fresh-frozen tissue sections) or 7 hr (FFPE) CODEX (PhenoCyler™) staining process with ease and precision. With optional antibody screening mode!
- [CODEX Reagent Setup](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/copy-of-codex-phenocyler-tm/codex-reagent-setup.md)
- [Temperature-controlled incubations](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/temperature-controlled-incubations.md)
- [Page 2](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/page-2.md)
- [ParheliaBio.com content](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content.md): Training Data and content from https://parheliabio.com/
- [Advanced Tissue Staining Solutions | ParheliaBio](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/advanced-tissue-staining-solutions-or-parheliabio.md)
- [Omni-Stainer™ S12 - Automation Bundle](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/omni-stainer-tm-s12-automation-bundle.md)
- [Omni-Stainer™ S12 - Manual Operation Bundle](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/omni-stainer-tm-s12-manual-operation-bundle.md)
- [Shop](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/shop.md)
- [Omni-Stainer™ S12 Thermal Sheath](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/omni-stainer-tm-s12-thermal-sheath.md)
- [Omni-Stainer™ C12 - Automation Bundle](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/omni-stainer-tm-c12-automation-bundle.md)
- [Omni-Stainer™ C12 Thermal Sheath](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/omni-stainer-tm-c12-thermal-sheath.md)
- [Consumables Archives](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/consumables-archives.md)
- [Conditioning Reagent 5ml Bottle](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/conditioning-reagent-5ml-bottle.md)
- [Omni-Stainer™ C12 - Manual Operation Bundle](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/omni-stainer-tm-c12-manual-operation-bundle.md)
- [S12 Coverpads - 48 Pack](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/s12-coverpads-48-pack.md)
- [C12 Filter Paper](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/c12-filter-paper.md)
- [Opentrons Robots Archives](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/opentrons-robots-archives.md)
- [S12 Filter Paper](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/s12-filter-paper.md)
- [C12 Support Pad - 48 Pack](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/c12-support-pad-48-pack.md)
- [Opentrons OT-2 Liquid Handling Robot](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/opentrons-ot-2-liquid-handling-robot.md)
- [Opentrons Single-Channel Electronic Pipette p20 (GEN2)](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/opentrons-single-channel-electronic-pipette-p20-gen2.md)
- [Opentrons 300 µl Pipette Tip Tip Racks - 9600 tips](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/opentrons-300-l-pipette-tip-tip-racks-9600-tips.md)
- [Greater Tissue Staining Workflow Efficiency. Slide Staining Kits](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/parheliabio.com-content/greater-tissue-staining-workflow-efficiency.-slide-staining-kits.md)
- [Opentrons setup guides](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/opentrons-setup-guides.md): Content from support.opentrons.com
- [Opentronssetupguides](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/opentrons-setup-guides/opentronssetupguides.md)
- [GetstartedImportaprotocol](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/opentrons-setup-guides/getstartedimportaprotocol.md)
- [More Parheliabio.com content](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/more-parheliabio.com-content.md)
- [Howitworks](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/more-parheliabio.com-content/howitworks.md)
- [Parhelia Biosciences FAQs](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/more-parheliabio.com-content/parhelia-biosciences-faqs.md)
- [Page 1](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/more-parheliabio.com-content/parhelia-biosciences-faqs/page-1.md)
- [Frequently asked questions parheliabio website](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/more-parheliabio.com-content/parhelia-biosciences-faqs/page-1/frequently-asked-questions-parheliabio-website.md)
- [ParheliaFrequentlyaskedquestions](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/more-parheliabio.com-content/parheliafrequentlyaskedquestions.md)
- [Parhelia Omni-Stainer FAQ](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/more-parheliabio.com-content/parhelia-omni-stainer-faq.md)
- [Meet your Parhelia Omnistainer](https://docs.parheliabio.com/background-knowledge-llm-semantic-training-data/background-info-and-lens-training-docs/meet-your-parhelia-omnistainer.md): This page uses some old nomenclature, such as Cover Tile instead of Cover Pad and Support Tile instead of Support Pad


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