ibidi Pump System Instruction Manual
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ibidi Pump System Instruction Manual

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Instruction Manual
ibidi Pump System
Version 2.6
ibidi.com

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Summary of Contents for ibidi ibidi Pump System

  • Page 1 Instruction Manual ibidi Pump System Version 2.6 ibidi.com...
  • Page 2 Pump System Contact ibidi GmbH Lochhamer Schlag 11 82166 Gr¨ a felfing Germany Phone: +49 89 / 520 46 17 - 0 Fax: +49 89 / 520 46 17 - 59 E-mail: info@ibidi.de Internet: ibidi.com Version 2.6 (May 12, 2022)

  • Page 3: Table Of Contents

    ........2 Intended Use of the ibidi Pump System 3 Equipment 3.1 Components of the ibidi Pump System...
  • Page 4 ......5.5 Connecting the ibidi Pump to the Computer ......
  • Page 5 ..........8.5 Shear Stress Calculations in ibidi Channel Slides .
  • Page 6 ......10.5 No Connection Between ibidi Pump and PumpControl Software ... . .

  • Page 7: Preamble

    1 Preamble 1.1 Introduction This manual is your guide to using the ibidi Pump System for flow experiments with the ibidi Chan- nel Slides. It instructs first–time users how to use the instrument, and serves as a reference for expe- rienced users.

  • Page 8: Nomenclature

    Pump System 1.3 Nomenclature ibidi Pump Fluidic Unit 1.4 Specifications Table 1: Specifications of the ibidi Pump System Electrical Specifications Power Supply Protection class Ingress protection rating IP 20 Overvoltage category External power supply AC 100–240 V, 50/60 Hz, 36–40 W Input line voltage and current ibidi max.
  • Page 9 Electrical cable (FU to pump) 2.0 m Air pressure tubing 2.0 m Air pressure tubing drying bottle 2.1 and 0.6 m Pressure Range of the ibidi Pump Total pressure range 0-100 mbar Recommended pressure range 5-95 mbar Electrical Input Fluidic Unit...

  • Page 10: Disclaimer

    Pump System 1.5 Disclaimer • ibidi shall not be held liable, either directly or indirectly, for any damage incurred as a result of product use. • The contents of this manual are subject to change without notice for product improvement.
  • Page 11 • Avoid vibrations from vacuum pumps, centrifuges, electric motors, processing equipment, and machine tools. • Avoid dust and corrosive gas. Do not install the ibidi Pump System where it could be exposed to high levels of dust or to outside air or ventilation outlets.

  • Page 12: Limited Warranty

    1.8 Transporting the ibidi Pump System The weight of the ibidi Pump is approx. 3 kg/6.6 lbs. The weight of the Fluidic Unit is approx. 1.1 kg/2.4 lbs. Moving the devices during operation will pose a risk of personal injury or damage to the instrument.

  • Page 13: Waste Disposal - Weee/Rohs Compliance Statement

    Hazardous Substances, RoHS). 1.10.1 EU Directive WEEE The ibidi Pump System must be disposed of in compliance with the WEEE Directive 2012/19/EC. This symbol on the product is in accordance with the European Union’s Waste Electrical and Elec- tronic Equipment (WEEE) Directive.

  • Page 14: Regulatory Statement

    Any modification to the product, not authorized by us, will invalidate this declaration. Laborgerät / laboratory equipment: ibidi Pump System ibiPump 2 Der oben beschriebene Gegenstand erfüllt die Vorschriften der Richtlinie 2011/65/EU vom 08. Juni 2011 zur Beschränkung der Verwendung bestimmter gefährlicher Stoffe in Elektro- und Elektronikgeräten.

  • Page 15: Intended Use Of The Ibidi Pump System

    • Minimization of the medium consumption with a circulating medium flow. • Minimization of mechanical stress on suspended cells to avoid destruction and non-specific cell-activation. The ibidi Pump System is for research use only! It is not intended for use in diagnostic procedures. Instruction Manual Version 2.6 (May 12, 2022)

  • Page 16: Equipment

    Pump System 3 Equipment The ibidi Pump System consists of the ibidi Pump, the Fluidic Unit(s), and disposable parts, such as Perfusion Sets and Slides. 3.1 Components of the ibidi Pump System An overview of the different ibidi Pump System versions is given in this section. Table lists all available options of the ibidi Pump System.

  • Page 17: Ibidi Pump

    • Sterile µ-Slides Luer Type 3.2 ibidi Pump The ibidi Pump can generate air pressure up to 100 mbar. The most precise working range is 5 to 95 mbar. Additionally, the pump can set the air flow direction. When using positive pressure, the pump will expel air from the front port, and intake it from the rear port.

  • Page 18: Fluidic Unit

    Air Pressure Pump 2 Rear air inlet Power connector Figure 2: Rear view of the ibidi Pump with rear air port, USB and power supply port, and Fluidic Unit cable ports. 3.3 Fluidic Unit The Fluidic Unit holds the Perfusion Set (fluidic reservoirs and tubing), and performs the switching operations to generate the unidirectional constant flow in the flow chamber.
  • Page 19 Pump System Figure 3: Front and back view of the Fluidic Unit. The Fluidic Unit can be equipped with a choice of one of three holder sizes, for the respective syringe reservoir sizes. The Reservoir Holder can easily be exchanged by the user. The standard reservoirs are indicated in Table on page 22.

  • Page 20: The Valve Block

    Perform the pinch test and observe the actuation of the bar in the pinch valve. If you see the bar moving inside the valve and the pinch test is ok, the valve works properly. If not, contact ibidi or your local supplier for repair. Version 2.6 (May 12, 2022)

  • Page 21: Perfusion Sets

    Pump System 3.4 Perfusion Sets The disposable Perfusion Sets are supplied in a gas-permeable sterile package. The tubing is color- coded for easy identification. The Perfusion Sets are specifically designed for use with the Fluidic Unit. However, the Luer adapters can be connected to any suitable flow chamber with Luer connec- tors.

  • Page 22: Ibidi Μ-Slides

    Elbow Luer Connector Male µ-Slide 3.5 ibidi µ-Slides For flow applications, µ-Slides with different coatings and characteristics are available. All ibidi Channel Slides provide female Luer adapters for an easy connection to any flow setup via standard male Luer connectors (see flow accessories on the ibidi website).
  • Page 23 Pump System The µ-Slide VI provides six independent channels for general flow assays. It is also available as a glass bottom version (see Table 9). The µ-Slide VI provides six independent micro-channels for general flow assays. The µ-Slide I Luer 3D is designed for perfusing a cell monolayer on a gel matrix.
  • Page 24 Pump System Table 9: Overview of all available ibidi channel slide geometries with medium volumes and areas. ibidi Channel Slides Channel Channel Growth Coating Height Volume Area Area µ-Slide I Luer 0.2 mm 50 µl 2.5 cm 5.2 cm µ-Slide I...

  • Page 25: Slide And Perfusion Set Selection Guide

    Please find a detailed overview of the minimal and maximal flow rates and shear stresses that can be applied with the ibidi Pump System in the following tables. The minimum and maximum values are based on the minimal working pressure of 5 mbar, and the maximal working pressure of 95 mbar.
  • Page 26 Pump System Perfusion Set Yellow/Green Flow rate Shear stress Viscosity: 0.0072 dyn s/cm Min. Max. Min. Max. Temperature: 37°C Without any slide 3.1 ml/min 36.0 ml/min – – µ-Slide I Luer 1.7 ml/min 22.0 ml/min 6.1 dyn/cm 78.0 dyn/cm µ-Slide I...
  • Page 27 Pump System Perfusion Set Blue Flow rate Shear stress Viscosity: 0.0072 dyn s/cm Min. Max. Min. Max. Temperature: 37°C Without any slide 0.82 ml/min 10.0 ml/min – – µ-Slide I Luer 0.65 ml/min 8.0 ml/min 2.4 dyn/cm 28.0 dyn/cm µ-Slide I...
  • Page 28 Pump System Perfusion Set Grey Flow rate Shear stress Viscosity: 0.0072 dyn s/cm Min. Max. Min. Max. Temperature: 37°C Without any slide 0.20 ml/min 2.9 ml/min – – µ-Slide I Luer 0.20 ml/min 2.9 ml/min 0.75 dyn/cm 10.4 dyn/cm µ-Slide I...
  • Page 29 Pump System Perfusion Set Black Flow rate Shear stress Viscosity: 0.0072 dyn s/cm Min. Max. Min. Max. Temperature: 37°C Without any slide 0.08 ml/min 1.10 ml/min – – µ-Slide I Luer 0.08 ml/min 1.10 ml/min 0.30 dyn/cm 3.90 dyn/cm µ-Slide I...

  • Page 30: Drying Bottle

    Pump System 3.7 Drying Bottle To supply CO -enriched air to the Fluidic Unit, the back port of the pump must be connected with a tubing to the incubator atmosphere. The drying bottle must be inserted into the tubing leading from the incubator to the pump to protect the pump from the incubator’s humidified atmosphere.

  • Page 31: Computer With Pumpcontrol Software

    Pump System 3.8 Computer with PumpControl Software The ibidi Pump is controlled by the PumpControl Software that is installed on a laptop or a desktop computer. Using a laptop configured and approved by ibidi will ensure that all settings are correct.
  • Page 32 Pump System 4 Quick Start Guide This section provides an overview for the standard setup components of the ibidi Pump System with one Fluidic Unit in an incubator. All steps are described in detail in Section and 6. 1. Place the pump on the working bench and connect the power supply.

  • Page 33: Basic Setup

    This section details how to connect all the components for a basic setup using a 10 ml Perfusion Set. For first-time users of the ibidi Pump System, it is recommended, to set up the system outside the incubator and practice using deionized water.

  • Page 34: Connecting The Fluidic Unit To The Pump

    Pump System When working with positive pressure, the atmosphere from the incubator is drawn in through the pump’s rear port to ensure a saturation of 5% CO . To prevent condensation inside the pump, a drying bottle (Section 5.3) is inserted. The setup is shown in figure 13. The modified setup for negative pressure is shown on page 62.

  • Page 35: Installing The Pumpcontrol Software

    Follow the instructions in Section 8.2. 5.4 Installing the PumpControl Software The PumpControl software comes pre-installed on the laptop that is delivered with the ibidi Pump System. If you need to install the software on a different computer, follow the instructions below.

  • Page 36: Connecting The Ibidi Pump To The Computer

    The power supply and the USB cable are included. For stability reasons, it is imperative to use the included power supply and USB cable. 1. Power up the ibidi Pump with the power supply. To verify that power is connected, check the “Power” LED status on the front panel (Figure 17).

  • Page 37: Setting Up An Experiment With Cells

    Pump System 6 Setting Up an Experiment With Cells This section explains all necessary steps to setup an experiment with cells and unidirectional flow. A more detailed cell culture protocol for performing an experiment with HUVEC under perfusion is provided in Application Note 13 “Endothelial Cells under...

  • Page 38: Mounting A Perfusion Set On The Fluidic Unit

    Pump System inside the slide and tubing. Degassing all plastic components before the experiment will eliminate this effect. Important! Each time you take the system out of the incubator, the process of gas absorption begins again. Therefore work quickly at room temperature and never leave the Fluidic Unit outside the incu- bator for longer than 10 minutes.
  • Page 39 Pump System Figure 20: Screw the adapters tight Figure 21: Secure the Luer adapters in the into the reservoirs. Female Luer Coupler. 3. Insert the reservoirs into the holder. The reservoir connected to the tubing with the extra red marking (reservoir B) must be inserted into the right side of the holder (viewed from the front).
  • Page 40 Pump System Figure 24: Insert the tubing coming from reservoir A into the left side slots. The marked tubing goes in the rear slot. 6. Check the correct position of the tubing in the openings of the pinch valve (Figure 25).

  • Page 41: Filling The Perfusion Set With Medium

    Pump System Figure 26: Move the tubing up and down while stretching for easy placement into the valve slots. 6.3 Filling the Perfusion Set with Medium To maintain sterility inside the Perfusion Set, do not disconnect any tubing adapter or reservoir filter outside the laminar flow hood.

  • Page 42: Remove Air Bubbles From The Perfusion Set

    Pump System Figure 28: Fill the syringe reservoirs with medium to equal levels and connect the filters to the reservoirs again. 6.4 Remove Air Bubbles from the Perfusion Set Once the system is set up and the Perfusion Set contains medium, air bubbles remaining in the branched tubing arms must be removed.

  • Page 43: Pinch Test

    Stretch the tubing and move it up and down for proper placement in the valve’s slot (Figure 26). Also check for correct positioning of the tubing (Figure 25). If this action does not correct the problem, contact ibidi or your local distributor. 6.6 Calibration of the Flow Rate The PumpControl software provides an automatic calculation of pressure, flow rate and shear stress, once the Perfusion Set, the slide and the viscosity of the medium are set.

  • Page 44: Connect The Calibration Slide To The Perfusion Set

    Pump System Figure 30: The correlations among pressure, flow rate and shear stress in the ibidi Pump System. Because of manufacturing tolerances, setup variations, and temperature fluctuations, the values for each Perfusion Set can differ from the values given in the software. To obtain the required experi- mental flow rate, we recommend performing a system fine calibration.

  • Page 45: Flow Rate Measurement

    Pump System Figure 32: Fill the reservoir before con- Figure 33: Connect the second Luer necting the Luer adapter. adapter to the µ-Slide. 6.6.2 Flow Rate Measurement Use a stop watch to measure and calibrate the flow rate. Important! The system must be calibrated with the same slide and pressure you want to use in your experi- ment.
  • Page 46 Pump System 5. Conduct at least four time measurements and calculate the mean value. If necessary, perform more measurements to optimize your measurement error. 6. To calculate the flow rate [ml/min], insert the time that was measured (mean value in seconds) in the formula below.

  • Page 47: Flow Calibration In The Software

    Pump System 6.6.3 Flow Calibration in the Software Now use the measured flow rate to update the PumpControl software in the “Recalibration factor” menu. 1. Click on the “Recalibration factor” button to open the dialog (Figure 35). 2. Insert the given flow rate and the one that was measured of yourself in the recalibration dialog (Figure 35).

  • Page 48: Connect The Cell-Seeded Slide To The Perfusion Set

    To start flow, place the whole assembly (Fluidic Unit and slide) in the incubator and connect the Fluidic Unit to the pump (air pressure tubing and electric cable). Start the experiment in the ibidi Pump Control software by increasing the shear stress step by step until the target shear stress is...

  • Page 49: Medium Exchange

    Pump System 6.10 Medium Exchange A medium exchange is necessary when the nutrients in the medium are used up by the cells (pH) or if evaporation exceeds a certain level (e.g., 5%). When a medium exchange is necessary will depend on your setup.
  • Page 50 Pump System 4. Fill both reservoirs to the 5 ml (1 ml) mark with fresh medium. Figure 38: Complete medium exchange. Version 2.6 (May 12, 2022) Instruction Manual...

  • Page 51: Installation Of Special Setups

    • The drying bottle must be installed between the rear port of the pump and the incubator (Sec- tion 5.3). • Mount the Perfusion Sets as explained in Section 6.2. Figure 39: Connection of the ibidi Pump and four Fluidic Units via the Splitter Set for 4 Fluidic Units. Instruction Manual Version 2.6 (May 12, 2022)

  • Page 52: Flow Calibration Of Two Or More Fluidic Units

    Pump System 7.1.2 Flow Calibration Of Two or More Fluidic Units To calibrate a system running with more than one Fluidic Unit, we recommend measuring the flow rate of each Fluidic Unit separately. The flow calibration procedure is outlined in Section 6.6.

  • Page 53: Oscillatory Flow Experiments

    Pump System 7.3 Oscillatory Flow Experiments For oscillatory flow applications, at least two Fluidic Units are required (one “primary” and one “secondary”) to separate the switching events of the two valves (V1 and V2). The primary Fluidic Unit has a long switching time t...
  • Page 54 Pump System Figure 41: Preparation and parts to connect the Air Pressure Splitter Set for two Fluidic Units to the primary (1) and secondary (2) Fluidic Unit. Follow the steps below for correct installation. 1. Remove the short tubing that standardly connects the valve block (V1) to the tubing leading to the Perfusion Set.
  • Page 55 Pump System Important! If no unidirectional flow is needed, mount an empty Perfusion Set or insert some tubing pieces into the primary Fluidic Unit’s pinch valve (V2) to protect it. Figure 42: Setup of the oscillatory flow with two Fluidic Units (one primary (1) and one secondary (2)).

  • Page 56: Settings Within The Pumpcontrol Software

    Pump System 7.3.2 Settings within the PumpControl Software Because the switching times are different for the primary and the secondary Fluidic Units, the Pump- Control software must be programmed accordingly. Figure shows how to correctly set the corre- sponding parameters.
  • Page 57 Pump System Figure 44: Oscillatory flow setup with four Fluidic Units (one primary and three secondaries). Instruction Manual Version 2.6 (May 12, 2022)

  • Page 58: Pulsatile Flow Experiments

    Fluidic Unit will periodically interrupt to create pulsation. Follow the steps below for correct installation: 1. Connect the first Fluidic Unit to Port 1 and the second to Port 2 on the ibidi Pump. 2. Connect the air pressure tubing to the first Fluidic Unit only.
  • Page 59 Pump System Figure 46: PumpControl example setting for pulsatile flow. Note! Pulsatile flow experiments work best with Perfusion Sets with long tubing (50 or 100 cm). Instruction Manual Version 2.6 (May 12, 2022)

  • Page 60: Technical Details

    The pump supplies a constant air pressure to the reservoirs of the Fluidic Unit, which generates a constant flow of medium within the ibidi channel slides. Before the reservoir runs dry, the liquid is pumped back and forth between the two media reservoirs of the Fluidic Unit. To create a unidirec- tional flow, two valves, labeled (V1) and (V2), are integrated in the Fluidic Unit, which are switched simultaneously between two states (Figure 48).
  • Page 61 Pump System Figure 48: Working principle of the valves creating a unidirectional flow, using positive pressure. Example with positive pressure In State 1, the valve (V1) is set such that the pressurized air is applied to reservoir (A), while the outlet of reservoir (B) is opened to the atmosphere. This creates a flow from reservoir (A) to reservoir (B).

  • Page 62: Positive Versus Negative Air Pressure

    When using positive air pressure, the front port of the pump pushes out pressurized air. The ambient air is drawn into the ibidi Pump at the rear port. This means, that the air applied to the Fluidic Unit(s) is not enriched in CO .
  • Page 63 Pump System 1. Connect the end of the black-marked tubing to the Fluidic Unit (inside the incubator). 2. Connect the yellow-marked tubing to the pump front port. With negative air pressure, the ambient air that enters the reservoirs comes directly from inside the incubator and provides the correct CO concentration.

  • Page 64: Flow Characteristics

    Pump System 8.3 Flow Characteristics Because of the geometry of the setup, the flow within the tubing and the µ-Slide channel is laminar, independent of the flow rate and type (i.e., continuous, oscillatory or pulsatile). When working with positive pressure, the flow is from the right to the left side. (front view). Apply- ing negative pressure reverses the direction.

  • Page 65: Viscosity

    (1 mPa s = 0.01 dyn s/cm Figure 51: Viscosity of water as a function of temperature. 8.5 Shear Stress Calculations in ibidi Channel Slides The wall shear stress in a µ-Slide depends on the flow rate and the viscosity of the perfusion medium.
  • Page 66 Pump System µ-Slide I Luer Glass Bottom 104.7 µ-Slide I Luer 60.1 µ-Slide I Luer Glass Bottom 51.5 µ-Slide I Luer 34.7 µ-Slide I Luer Glass Bottom 31.0 µ-Slide VI 176.1 µ-Slide VI Glass Bottom 99.1 10.7 µ-Slide VI Version 2.6 (May 12, 2022)
  • Page 67 Pump System µ-Slide I Luer 3D 60.1 µ-Slide y-shaped 227.4 (single channel) µ-Slide y-shaped 113.7 (branched channel) 3in1 µ-Slide III 774.1 (1 mm channels) 3in1 µ-Slide III 227.4 (3 mm channel) Important! Note that the starting point for most experiments is the shear stress. Depending on the chan-...

  • Page 68: Working With Non-Implemented Flow Channels

    2. Calculate the flow rate required to obtain this shear stress in the specific slide geometry. 3. Measure a calibration curve with the slide and the ibidi Pump System (with Fluidic Unit and Perfusion Set), showing the dependence between flow rate and pressure.
  • Page 69 Pump System Figure 52: Example of a calibration curve showing the relation between flow rate and pressure. 4. This calibration curve enables the prediction of the pressure needed to generate the desired flow rate (p in mbar, in ml/min).
  • Page 70 Pump System 60 s/min 5 ml Switchingtime 60 s/min 5 ml 22.5s 13.3 ml/min Insert the value of 22 s in the box “Switching times, unidirectional” (slightly rounded down). Version 2.6 (May 12, 2022) Instruction Manual...

  • Page 71: Maintenance

    Pump System 9 Maintenance Although the ibidi Pump system requires minimal maintenance, there are some parts that will have to be checked occasionally. 9.1 Disinfection and Cleaning Pump Controller Unplug the external power supply cord from the ibidi Pump and electrical outlet.

  • Page 72: Troubleshooting

    Pump System 10 Troubleshooting It is helpful to locate an issue with the ibidi Pump System and find a solution, by starting with the failure description. Check the following subsections for the adequate failure description. When contacting the ibidi technical support for assistance, please provide the relevant log files.

  • Page 73: Cells Are Detaching

    Pump System Temperature changes along the tubing, Keep the temperature stable along the tubing, e.g., e.g., when parts of the tubing are led out- with a cage incubator with a temperature-controlled side an incubator. This can happen when atmosphere.

  • Page 74: Cells Detach Under Flow Conditions

    Pump System The cells were stressed by the abrupt tem- Avoid placing slides directly onto metal surfaces. For perature change from being placed onto best results, place slides on the ibidi µ-Slide Rack, or a the metal surface of the sterile working Petri dish.

  • Page 75: Medium Runs In One Direction Only

    Pump System Note! A slight imbalance is normal due to variance from fluid dynamics and in the valve switching events, and is tolerated, as long as the reservoirs do not run dry. Possible Cause Solution Incorrect insertion of the tubing in the Perform the pinch test (Section 6.5).

  • Page 76: No Connection Between Ibidi Pump And Pumpcontrol Software

    Unit and the reservoir. if necessary. Fluidic Unit is connected with the wrong Especially when working with the predefined setups, port on the back of the ibidi Pump con- check, that the Fluidic Unit is connected to the right troller. port.

  • Page 77: Flow Rate Is Too Low Or Absent

    Pump System Possible Cause Solution Blockage in the air pressure tubing lead- Make sure that the air tubes are not being squeezed ing from the pump to the drying bottle or and that there is no blockage inside the tubing. Es- from the drying bottle to the incubator.

  • Page 78: Total Medium Volume In The Perfusion Set Is Decreasing

    Pump System 10.9 Total Medium Volume in the Perfusion Set is Decreasing Issue: Long-term experiments could result in medium evaporation. The amount of volume loss per day depends on the humidity in the incubator and the volume flow rate. Do not exceed a volume loss of more than 10% of the total volume.
  • Page 79 USB cable is suitable, but when encountering connection issues make sure to use the USB cable de- livered with the ibidi pump or a double shielded USB cable with the following specifications: reversible A- male to B-male, 28AWG Data Pair, 24AWG Power pair, transfer rate up to 480 Mbps or more.
  • Page 80 GmbH Lochhamer Schlag 11 82166 Gräfelfing Germany Toll free within Germany: Phone: 0800 / 00 11 11 28 Fax: 0800 / 00 11 11 29 International calls: Phone: +49 89 / 520 46 17 - 0 Fax: +49 89 / 520 46 17 - 59 E-Mail: info@ibidi.com...

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