Welcome to Chips & Tips

Welcome to Chips & Tips – a unique and regularly updated forum for scientists in the miniaturisation field from Lab on a ChipChips & Tips aims to provide a place where ideas and solutions can be exchanged on common practical problems encountered in the lab, which are seldom reported in the literature.

Do you

  • have problems with bubble formation when injecting your sample?
  • wish there was a quicker way to make prototypes?
  • find connecting chips to pumps and syringes problematic?

Or do you have your own tricks to overcome problems like these?

If so, then Chips & Tips is the forum to address your requirements!  Read the Tips below or see the author guidelines on how to submit your own today.

Chips & Tips is moderated by Glenn Walker (North Carolina State University).

Please note that Chips & Tips before April 2011 were originally published at www.rsc.org.

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Daniel Alcaide Martín, Jean Cacheux, Sergio Dávila & Isabel Rodríguez

Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanoscience), Ciudad Universitaria de Cantoblanco, C/Faraday 9, Madrid 28049, Spain

1- Why is this useful?

Microfluidic devices need to be connected to fluidic pumps for regulation of the flow during the device operation1. Connecting and disconnecting devices is a tedious and time-consuming operation that often causes air bubbles which are detrimental for the fluidic experiment and a real nuisance for the time it takes to eliminate them.

Furthermore, in microfluidic experiments dealing with biomolecules or cell cultures, volumes are of concern as these materials are typically limited and/or costly. Hence, it will be very useful if the reagent filling or replacement process and the connecting and disconnecting operations to microchips are minimized to avoid both bubbles and reagents waste. Reducing the reservoir volume to the volumes needed for the experiment minimizing dead volumes will also allow saving expensive reagents.

With this aim, we have designed a fixture to make practical fluidic connections to a microchip from a pressure controller for fluidic control and device operations. It allows for easy opening and closing operations and for easy re-filling or replacement of the reagents into the microchannels without moving any tubing connection.

Here, we present a dual connector cum reservoir fixture as a practical and effective means to making fluidic connections onto polydimethylsiloxane (PDMS) microfluidic based chips. The fixture is completely built by stereolithography (SLA) 3D printing and includes two components: a piece including a reservoir with an O-ring slit and a cone shaped outlet as chip connector and, another piece that closes the reservoir and has a cone shaped inlet or air pressure connector.

This Chips and Tips builds on a previous approach,2 dealing with microchip fluidic fixtures using magnets. However, in this case, the reservoirs and release connection are moved off the chip which would be more practical to work with the chip on the microscope stage for real time observations. Moreover, it is adaptable for any chip design and particularly for microchips made in soft PDMS.


2- What do I need?

  • 3D design software.
  • SLA 3D printer.
  • Cubic magnets.
  • O-rings.


3 – What do I do?

We first digitally design the parts of the dual connector: the reservoir-chip connector and the reservoir-seal air pressure adaptor. See the drawing in Figure 1. The corresponding F3D files can be here downloaded.

In our design, the reservoir sits aside from the PDMS chip and it is connected to it through a standard tube fitted on to the connecting outlet. The reservoir-seal encloses the reservoir. Four permanent magnets are inserted in each of the two components to produce a magnetic compressive force onto the O-ring and a tight seal to allow for applying a controlled pressure to cause the reagent to flow at the desired rate into the microfluidic chip.

Once the components are printed, the magnets are inserted into the lateral slots. Then, the plastic tubes are connected to the chip inlets and outlets and to the reservoir chip connector. The reservoir is filled with the correct volume of reagent (in this design is 0.2 ml) and the reservoir- seal piece is placed on top. Finally, through the air pressure inlet, tubing is connected to a pressure controller. When air pressure is applied, the reagent flows through the chip. The closing system formed by the O-ring seal and magnet force is able to handle at least 1 bar working pressure without any leakage.

Figure 2 – Fluidic system set-up showing .two dual connector-reservoir fixtures connected to a microchip and to a pressure controller.


This work was performed within the framework of the EVONANO project funded by the European Union’s Horizon 2020 FET Open programme under grant agreement No. 800983.


  1. Interfacing of microfluidic devices – Chips and Tips. https://blogs.rsc.org/chipsandtips/2009/02/27/interfacing-of-microfluidic-devices/.
  2. Reusable magnetic connector for easy microchip interconnects – Chips and Tips. https://blogs.rsc.org/chipsandtips/2011/06/27/reusable-magnetic-connector-for-easy-microchip-interconnects/.


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Solvent Extraction of 3D Printed Molds for Soft Lithography

Jonathan Tjong1, Alyne G. Teixeira1 and John P. Frampton1,2

1School of Biomedical Engineering, Dalhousie University, Halifax, NS, Canada

2Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada

Why Is This Tip Useful?

Casting polydimethylsiloxane (PDMS) in molds produced from additive manufacturing (i.e., 3D printing) enables rapid prototyping of parts with microscale features without the need for conventional photolithography. Whereas conventional photolithography followed by soft lithography involves the use of silicon substrates and photomasks, which can be costly and may require special preparation and processing (e.g., application and removal of photoresist in a clean room environment), the emergence of stereolithographic 3D printers allow for the rapid manufacture of masters for PDMS casting in almost any laboratory space. Stereolithographic 3D printers use photopolymer resins that when cured can withstand temperatures as a high as 200 °C without plastic deformation, which occurs with thermoplastics such as polystyrene that have glass transition temperature around 95-105 °C (Lerman et al.). The ability to withstand such high temperatures opens the possibility for PDMS and other silicone elastomers to be cured quickly and also provides the possibility for greater control of the mechanical properties of the elastomers (Johnston et al.). However, the components within the 3D printed resin mold such as residual photoinitiators and unreacted oligomers may interfere with the curing of PDMS, resulting in incomplete curing at the interface of the printed mold and the PDMS part. Here, we demonstrate a simple treatment to remove these unwanted materials through solvent extraction.

What Do I Need?

  • Stereolithographic 3D printer and appropriate resin
  • Leak-proof, sealable container large enough to hold the 3D-printed mold
  • Dishwashing detergent
  • 95% ethanol or isopropanol
  • Orbital shaker table
  • Uncured PDMS base and curing agent (10:1 w/w)
  • Post-curing UV lightbox

What Do I Do?

  1. After cleaning and post-curing of the 3D-printed mold in the UV lightbox, place the mold in the container and add enough solvent to submerge the part.
  2. Seal the container and leave on a shaker table for 24 hours.
  3. Discard the old solvent and add new solvent. Seal and agitate for another 24 hours.
  4. Remove the part from the solvent and allow to air dry at room temperature.

What else should I know?

The exact composition of photopolymer resins for stereolithography may vary significantly between different manufacturers; therefore, it may be necessary to adjust the protocol (e.g., the type of solvent). In addition, larger prints will likely require more solvent and a longer duration of solvent extraction to account for the increased migration time of unwanted components from the print to the free solvent.

To demonstrate our procedure, we printed two sets of 5 identical molds with basic geometric features. One set used 1 mm thick outer walls, while the other set used 3 mm thick outer walls (Figure 1). The molds were designed using Onshape (Onshape, Cambridge, MA) CAD software and printed using a B9Creator v1.2 (B9Creations, Rapid City, SD) stereolithographic 3D printer. For all prints, we used B9-R2-Black resin from B9Creations. This resin is documented by the manufacturer as having a heat deflection temperature of 65 °C at 0.45 MPa determined through ISO 75-1/2:2013 standards (B9Creations). As no significant mechanical load would be placed on the resin molds (with a maximum depth of 6 mm for the PDMS chamber), we decided this resin was suitable for our test molds. After printing, excess resin was removed from the molds by submerging and agitating in an approximately 1:10 mixture of Dawn dishwashing detergent and water in a 1 L container. This was followed with additional cleaning by rinsing with excess isopropanol using a wash bottle until no visible evidence of uncured resin was present on the surface (approximately 10-20 mL per part). The molds were then post-cured in a UV lightbox for 20 minutes.

Once post-cured, the molds were each placed in new, 15 mL polypropylene centrifuge tubes (Falcon® Corning, Corning, NY) with 10 mL of the test solvents (reverse osmosis-treated (RO) water, isopropanol, 95% ethanol, or methanol), and exposed to the two 24-hour extraction procedures listed in the “What Do I Do” section. After extraction, the molds were briefly rinsed with RO water and allowed to air dry for 1 hour. Then, approximately 0.4 mL or 1 mL of premixed 10:1 uncured PDMS and curing agent were added to the 1 mm and 3 mm molds, respectively. The PDMS parts were heat-cured in a dry oven at 65 °C overnight. The cured PDMS parts were then carefully removed from the mold using a stainless-steel spatula. Images were taken using the default settings on an iPhone 7 camera.

Resin molds that did not undergo extraction or that underwent extraction in water or methanol produced PDMS parts with major defects. For these extraction conditions, fragments of semi-cured and traces of uncured PDMS remained at the PDMS-mold interface (Figure 2A-C). Extraction with methanol appeared to weaken the cured resin, with significant softening and the appearance of cracks on these molds (Figure 2C), and while the cured PDMS easily released from the methanol-extracted molds, this left artifacts on the PDMS surface. We found that resin parts pretreated with either isopropanol or 95% ethanol performed well as molds for PDMS. The cured PDMS parts easily released from the substrates, with no visible traces of uncured PDMS (Figure 2D-E), and the PDMS parts we retrieved cleanly replicated the features of the resin mold (Figure 3). In addition to producing defects in the mold itself, extraction with methanol also led to bubbles forming in the PDMS as it cured (Figure 3C). Overall, PDMS casts were most easily released from the 1 mm-thick molds compared to the 3 mm-thick molds, but this may simply be due to the lower aspect ratio (h/l) of the 1 mm-thick molds.

Take Home Message

When casting PDMS parts from molds produced by stereolithography, incomplete curing and defects in the PDMS part can be minimized by extracting residual photo-initiators and oligomers present in the mold using either isopropanol or 95% ethanol.





B9Creations. Black Resin Material Properties. 2018, pp. 9–11, https://cdn2.hubspot.net/hubfs/4018395/Material Data Sheets/B9Creations Black Material Properties.pdf.

Johnston, I. D., et al. “Mechanical Characterization of Bulk Sylgard 184 for Microfluidics and Microengineering.” Journal of Micromechanics and Microengineering, vol. 24, no. 3, 2014, doi:10.1088/0960-1317/24/3/035017.

Lerman, Max J., et al. “The Evolution of Polystyrene as a Cell Culture Material.” Tissue Engineering – Part B: Reviews, vol. 24, no. 5, 2018, pp. 359–72, doi:10.1089/ten.teb.2018.0056.




Figures and Legends


Figure 1. Design features of molds produced by stereolithography. Top panels in (A) and (B) are the Onshape renderings. Bottom panels in (A) and (B) are parts printed in the B9Creations B9-R2-Black resin.

Figure 2. Molds produced by stereolithography following extraction in various solvents. Fragments of partially cured PDMS and uncured PDMS remain on the surface of molds that have not undergone extraction, as well as those extracted in RO-water and methanol. Isopropanol and 95% ethanol extraction produce molds that can be re-used numerous times for PDMS curing.

Figure 3. PDMS parts obtained from curing in resin molds extracted using various solvents. Extraction of residual photo-initiators and oligomers present in the mold prior to soft lithography using either isopropanol or 95% ethanol results in clean PDMS parts that are free of defects.

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Cutting the cords: Two paths to well-plate microfluidics

Sara E. Parker1 and Peter G. Shankles2, Maddie Evans1, Scott T. Retterer1,2,3

1 Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN

2 The Bredesen Center, The University of Tennessee, Knoxville, TN

3 The Center for Nanophase Materials Sciences

Why is this useful?

Even simple microfluidic devices often require complex and expensive pumping and valving systems for accurately metering and controlling fluid flow. This often necessitates substantial and time-consuming set-up, and sometimes make these chips unwieldly and difficult to image. It can also represent a significant departure from the rather straight forward process of pipetting fluids from one small volume to another, making adoption by non-microfluidic experts unlikely. However, the development of well-plate microfluidics1,2 provides a high throughput, simplified method for studying fluid exchange and shear flow, while minimizing the set-up and need for multiple fluid connections. Creating an interface between the polystyrene (PS) plate and the polydimethylsiloxane (PDMS) fluidics presents the largest obstacle in creating these hybrid devices. Khine et al.1 utilized pressure to create a tight interface while Conant et al.2 adhered the surfaces using glue, but neither elaborated on their techniques and in practice small changes in the process can result in failed devices. Here, two techniques are detailed on consistently creating an effective interface between the well-plate and microfluidics. Resulting in individual wells that are interconnected via custom microchannels in a PDMS device attached to the bottom of the well-plate. Reagents are then added to wells and, driven through the underlying channel network into an outlet well via hydrostatic pressure or a pressure control system3,4.

With the use of this platform, flow can be introduced into traditional well-plate studies allowing various physiological conditions to be more closely mimicked. Further, the compatibility of these custom devices with well-plate microfluidic control systems provides the opportunity to precisely and dynamically control experimental conditions including temperature, pressure, and gas environment3,4. The use of multi-well plates also allows for multiple devices to be bonded in parallel to the same plate, increasing throughput without increasing the complexity of the control system5. Additionally, the familiarity and ubiquity of the well-plate platform provides a familiar platform for technical professionals within the lab and is automatically compatible with the host of microscope stage attachments already available for use with conventional well-plates.

Well-plate microfluidic fabrication has been shown with a pressure seal between the microfluidics and well-plate1 as well as gluing the two together2. This work builds off these ideas by detailing bonding with a liquid adhesive or chemical activation and bonding. The process of bonding customized PDMS devices to well-plates for well-plate microfluidics has only been vaguely described previously5,6. Herein, we present two approaches that utilize either (3-Aminopropyl)triethoxysilane (ATPES) to modify the surface of the PS well-plate to bond with plasma treated PDMS, or uncured PDMS to act as a glue between the PS and PDMS surfaces7. While the APTES modification provides a stronger bond without adding additional material, the uncured PDMS bonding procedure requires less pressure, avoiding any distortion of nanoscale features. An overview of the process is shown in Figure 1:

Figure 1 – Diagram of the fabrication process with the APTES process above and PDMS glue below.

What do I need?


  • PDMS device replica with inlets and outlets designed to align with a well-plate
  • 48 well-plate; Flat-bottomed, non-tissue culture treated
  • Isopropyl alcohol (IPA)
  • Coverslip or slide large enough to cover channels
  • X-Acto knife
  • Scotch tape

APTES bonding only

  • Deionized water
  • Hard rubber brayer
  • Sealable plastic container

PDMS bonding only

  • Tapered tip plastic syringe (Nichiryo 6mL syringe with tips)
  • Uncured PDMS (10:1 w/w elastomer base to curing agent)


  • Drill press
  • Plasma cleaner (Harrick Plasma, Basic plasma cleaner PDC-32G)
  • Hot plate
  • Oven (75°C)

What do I do?

Well-plate preparation (for both bonding methods)

  1. Prepare the well-plate by drilling a hole in the center of each well corresponding to an inlet or outlet on the PDMS replica (Figure 2).
  2. Using an X-Acto knife, clean the edges of the drilled holes such that the bottom surface of the well-plate is smooth and any lips that may have formed from drilling have been removed.

Figure 2 – The prepared PDMS device is shown in a. and the prepared well-plate is shown in b.

APTES bonding Procedure

Well-plate APTES modification

1.      Clean the bottom surface of the well-plate with IPA and expose to oxygen plasma on high setting for 2 minutes, with the bottom surface of the plate facing up (Figure 3a).

2.      In a fume hood, prepare a 100 mL aqueous solution of 1% v/v APTES and pour the solution into a shallow, resealable container.

3.      Place the plasma treated well-plate in the APTES container so that the bottom surface of the plate is completely submerged. Seal the container and let soak for 30 minutes (Figure 3b)

4.      Remove the plate from the APTES bath and rinse the top and bottom with water. Dry the well-plate using compressed air and place it on a 50°C hot plate to ensure thorough drying.

Figure 3 – The well-plate was exposed to air plasma and submerged in a water/APTES solution to modify the surface chemistry and enable bonding between PS and PDMS. A coverslip was then plasma bonded to the PDMS surface.


1.      Clean the top of the PDMS replica (opposite to the channels) using scotch tape and plasma clean on high for 1 minute.

2.      With the channeled side of the PDMS replica facing up, align the inlets/outlets of the replica with the holes of the APTES-modified well-plate and press the layers together. Roll a brayer over the surfaces to remove any bubbles and ensure an even, uniform bond. Bake at 75°C for 20 minutes (Figure 3c).

3.      Remove the well-plate with bonded device from the oven and use scotch tape to remove debris from the channel-exposed PDMS. Clean a glass coverslip with IPA and expose the coverslip and well-plate to oxygen plasma on high for 1 minute. Bond the coverslip to the PDMS replica, thus enclosing the channels and bake at 75°C for 20 minutes.

Uncured PDMS procedure

1.      Remove any dust from the bottom (channel-exposed) side of the PDMS replica using Scotch tape and clean a glass coverslip with IPA. Expose both to oxygen plasma for 1 minute on high setting and bond them together, enclosing the channels. Bake at 75°C for 1 hour (Figure 4a).

2.      Clean the bottom surface of the prepared well-plate with IPA. Using the tapered tip syringe, place small droplets of uncured PDMS onto the bottom surface of the well-plate where the PDMS device will be bonded (Figure 4b).

3.      Using scotch tape, remove any dust from the top (opposite to the channels) of the coverslip-bonded PDMS replica. Align the inlets/outlets of the device with the holes of the well-plate and lightly press the device onto the well-plate (Figure 4c). Remove any uncured PDMS that may have leaked into the wells or inlets/outlets of the device. Bake at 75°C for 1 hour.

Figure 4 – The PDMS device was first bonded to a coverslip (a) and then bonded to a well-plate using uncured PDMS (b). c shows the completed device from the top and side view.


We present two methods for attaching PDMS microfluidic devices to polystyrene well-plates, providing the opportunity to utilize customized channels for well-plate microfluidics. Assays using these devices can be run in conjunction with well-plate microfluidic controllers or using simple pipetting methods by adding the desired reagent or media to the inlet wells (Figure 9). While the fabrication process is more involved than typical PDMS processing, well-plate microfluidics removes the need for complicated tubing connections by working with a single manifold controller, or hydrostatic flow using the well height to produce pressure.


1         M. Khine, C. Ionescu-Zanetti, A. Blatz, L. P. Wang and L. P. Lee, Lab Chip, , DOI:10.1039/b614356c.

2         C. G. Conant, M. A. Schwartz, J. E. Beecher, R. C. Rudoff, C. Ionescu-Zanetti and J. T. Nevill, Biotechnol. Bioeng., , DOI:10.1002/bit.23243.

3         Fluxion, White Pap., 2008, 1–6.

4         2012, US00825796.

5         C. G. Conant, J. T. Nevill, M. Schwartz and C. Ionescu-Zanetti, J. Lab. Autom., 2010, 15, 52–57.

6         P. J. Lee, N. Ghorashian, T. A. Gaige and P. J. Hung, J. Lab. Autom., , DOI:10.1016/j.jala.2007.07.001.

7         V. Sunkara, D.-K. Park, H. Hwang, R. Chantiwas, S. a. Soper and Y.-K. Cho, Lab Chip, 2011, 11, 962–965.


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A second life for old electronic parts: a spin coater for microfluidic applications

Gabriele Pitingolo1, Valerie Taly1 and Claudio Nastruzzi2

1INSERM UMR-S1147, CNRS SNC5014; Paris Descartes University, Paris, France. Equipe labellisée Ligue Nationale contre le cancer.

2Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italia

*Email: gabriele.pitingolo@parisdescartes.fr, nas@unife.it

Why is this useful?

It is well known that the rapid proliferation of information and communications technologies (ICT) has resulted in a global mountain of high-tech trash (e-waste). The problem with e-waste is not only the accumulation of electronic products and therefore the high disposal costs, but rather the hazardous substances present in their various components. Therefore, the importance of recycling is evident in the area of resource and energy conservation, finding a new, second life for electronic components.

Spin coaters are widely used instruments useful to deposit uniform thin films to flat substrates [1]. In microfluidics, the spin coating is used to coat a photoresist layer (such as SU-8) or to bond separate substrates by using the adhesive properties of PDMS. The spin coating technology is also used to fabricate thin polymer membranes. PDMS membranes are, for example, employed for a wide range of applications due to their several advantages. For instance, being PDMS membrane permeable, they can be used to exchange gas (in cell culture application for example) or small molecule (in filtration application) [2]. In addition, as recently reported, spin coating is suitable to fabricate microchannels with a circular section [3].

Unfortunately, most commercial spin coaters are expensive (£2,000-6,000) and possess some unwanted or redundant specifications, not necessarily needed for the fabrication/modification of microfluidic devices.

In this respect, we present here a tip to develop portable spin coaters by recycling computer fans and mobile phone wall chargers. The most common fans in personal computers have a size of 80 mm, but the size can range from 40 to 230 mm. It’s also known that the fans of different size show also a different rotational speed. Typically, the 80 mm fans have a rotational speed of 2000 rpm (that represent a suitable speed for common thin layering in microfluidics).

What do I need?

Parts for the spin coater

  • Personal computer fan
  • Insulated male/female wire pin connectors
  • Tesa power strip
  • Wall chargers from (old) mobile phones

Parts and chemicals for the specific examples

  • Milled poly(methyl methacrylate) (PMMA) microchannel
  • Glass slide
  • Sylgard® 184 silicone elastomer kit
  • Clumps

What do I do?

Assembling of spin coater

1.Remove the fan from an old pc (or mac, if are particularly posh) (Fig.1).

2. Connect the wall charger and the fan wires with insulated female and male wire pins. Afterwards, to turn on the fan, connect the female and male pins.

3. Using the tesa power strips, secure the substrate (i.e. glass slide or PMMA microchannel) to the central part of the fan (left picture). For devices larger than the fan, use an adeguate plastic stopper to elevate the device (right picture).

4. Drip, by a (micro)pipette, the liquid containing the coating material on top of the substrate.

5. Turn on the fan and spin coat the substrate for about 30 seconds (time can vary depending on the substrate viscosity and coating thickness required).

6. Verify the coating by peeling off the PDMS membrane from the glass slide by tweezer (left picture) or analyze the microchannel profile by microscopy (right panels).

What else should I know?

In this tip a portable spin coater for microfluidic applications was developed using old electronic parts. A single fan can be re-used many times (up to hundreds in our experience). The amount of PDMS (in form of droplets) falling on the fan is quite limited. If necessary the fan can be cleaned after any use by simply rubbing it with a wipe soaked with some petroleum ether (aka liquid paraffin or white petroleum). In the worst cases (very rarely occurring) the fan can be easily replaced, since they are available for free by any old unused PC.


This work was supported by the Ministère de l’Enseignement Supérieur et de la Recherche, the Université Paris-Descartes, the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé et de la Recherche Médicale (INSERM). This work was founded by CAMPUS FRANCE (n° 39525QJ) and carried out with the support of the Pierre-Gilles de Gennes Institute equipment (“Investissements d’Avenir” program, reference: ANR 10-NANO 0207). Financial support from the Università italo-francese grant G18-208 is gratefully acknowledged.


[1]          D. B. Hall, P. Underhill, and J. M. Torkelson, “Spin coating of thin and ultrathin polymer films,” Polymer Engineering & Science, vol. 38, no. 12, pp. 2039-2045, 1998.

[2]          S. Halldorsson, E. Lucumi, R. Gómez-Sjöberg, and R. M. Fleming, “Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices,” Biosensors and Bioelectronics, vol. 63, pp. 218-231, 2015.

[3]          R. Vecchione, G. Pitingolo, D. Guarnieri, A. P. Falanga, and P. A. Netti, “From square to circular polymeric microchannels by spin coating technology: a low cost platform for endothelial cell culture,” Biofabrication, vol. 8, no. 2, pp. 025005-025005, 2016 May 2016.

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Development of a cell culture microdevice with a detachable channel for clear observation

Eriko Kamata, Momoko Maeda, Kanako Yanagisawa, Kae Sato*

Department of Chemical and Biological Sciences, Faculty of Science, Japan Women’s University, Bunkyo, Tokyo 112-8681, Japan

*E-mail: satouk@fc.jwu.ac.jp

Why is this useful?

There have been many reports on microfluidic devices for cell culture having upper and lower microchannels separated by a thin PDMS membrane. In these devices, the lower channel often interferes with the microscopic observation of cells cultured in the upper channel. To avoid interference, a microdevice with a detachable lower channel was developed.

What do I need?


PDMS (SILPOT 184w/c, Dow Corning Toray)


PMMA sheet (56 × 76 × 2 mm)

Glass slides (52 × 76 mm and 26 × 76 mm)

Cover slip (24 × 60 mm)

1 kg weight

PTFE tubing (1 × 2 mm and 0.46 × 0.92 mm)

Tygon tubing (1.59 × 3.18 mm)

Biopsy Punches (1 mm and 2 mm, Kai corporation)


Vacuum desiccator

Oven (65 ˚C and 100˚C)

Spin coater

Plasma generator

Vacuum pump

What do I do?

  1. PDMS molding

Mix the elastomer and curing agent at a 10:1 mass ratio. De-gas the mixture under vacuum until no bubbles remain (20 min). Pour the degassed PDMS mixture onto a master, which has an upper channel (1 × 1 × 10 mm) or a lower channel (0.5 × 2 × 15 mm) structure, and then place it in an oven at 65˚C for 1 h. Peel off the PDMS replica from the master and adhere it to a glass slide (26 × 76 mm). Place it in an oven at 100˚C for 1 h (Fig.1).

  1. Preparation of a thin PDMS membrane

Spin coat 600 µL of the PDMS prepolymer (at a 10:1 mass ratio) on a PMMA sheet at 500 rpm for 20 s followed by 2,400 rpm for 600 s. Bake it at 65˚C for 1.5 h.

Fig.1 PDMS sheet with the upper channel, that with the lower channel, PDMS membrane, and tubing.

  1. Permanent bonding of the PDMS membrane and the sheet with the upper channel

Punch the inlet and outlet holes at both the ends of the upper channel with a 2-mm biopsy punch. Expose both the bonding surfaces of the PDMS membrane and the PDMS sheet with the upper channel (upper sheet) to plasma at 100 W, 35 s (Fig.2a and 2b). Laminate and bake them at 65˚C for 1 h (Fig.2c). Remove the PMMA sheet, and punch a hole to connect the sheet with the lower channel by using a 1-mm biopsy punch from the membrane side.


Fig.2 (a) Schematic diagram of bonding the PDMS membrane and the upper sheet. (b) Plasma treatment. (c) Bonded PDMS membrane and sheet.

  1. Detachable bonding of the PDMS membrane and the PDMS sheet with the lower channel

The PDMS sheet with the lower channel (lower sheet) is bonded to the PDMS membrane by using a PDMS prepolymer diluted with hexane (a dilution ratio of 1:3) as a glue1 (Fig.3a). Spin coat the diluted PDMS prepolymer (600 µL) at 2,000 rpm for 30 s on the surface of a glass slide (52 × 76 mm) to cover the slide with a thin layer of the glue and incubate it for 10 min to dry the solvent (Fig.3b). Place the lower sheet on the coated glass slide (Fig.3c). Apply glue at the four corners of the PDMS membrane bonded with the upper sheet (Fig.3d). Peel off the lower sheet from the glass slide and place the glue-coated surface of the sheet on the PDMS membrane (Fig.3e). After 30 min of incubation, bond the lower sheet to a cover slip by plasma bonding. Place a 1-kg weight and a glass slide on the device and bake it at 100˚C for 1 h (Fig.3f).

Fig.3 (a) Schematic diagram of bonding of the PDMS membrane and lower sheet. (b) Spin coat the diluted PDMS prepolymer (glue). (c) Lower sheet is placed on the thin film of the diluted PDMS prepolymer. (d) The diluted PDMS prepolymer is applied on the four corners of the PDMS membrane. (e)The glue-coated surface of the lower sheet is placed on the PDMS membrane. (f) A weight and a glass slide are placed on the device to bake it at 100˚C.

  1. Tubing

Connect polytetrafluoroethylene (PTFE) tubes (1 × 2 × 100 mm) with Tygon tubes (1.59 × 3.18 × 10 mm) to the holes present at both ends of the upper microchannel. Connect a PTFE tube (46 × 0.92 × 150 mm) to the hole of the lower channel. Apply PDMS prepolymer at the root of the tubes, and then bake it at 100˚C for 1 h for firm connection (Fig.4a and b).

  1. Cell culture

Introduce a cell suspension into the upper microchannel, which is manually precoated with 0.1 mg/mL of fibronectin. Incubate the device at 37˚C with 5% CO2 for 16 h to allow cells to adhere to the bottom of the upper channel (surface of the PDMS membrane).

  1. Detachment of the lower sheet for cell observation

Remove the lower sheet from the device carefully (Fig.4c and d). Place the rest of the device on a cover slip for observation with an inverted microscope (Fig.4 f and h).

Fig.4 (a) The complete microdevice. (b) Side view of the microdevice. The cell culture channel (upper) is filled with water containing a red food color, while the lower channel is filled with water containing a blue food color. (c) and (d) The lower sheet is peeled off from the microdevice carefully. Phase contrast images of cells (e) before and (f) after detachment of the lower sheet. Fluorescent images of cells stained with CellTracker Red CMTPX (g) before and (h) after detachment.


We developed a microfluidic device with a detachable lower microchannel. It is important that different bonding techniques be used for each side of the PDMS membrane. If the lower channel is filled with air and the device is incubated in a CO2 incubator, dew condensation is often observed in the lower channel when the device is taken out from the incubator. The condensation in the lower channel makes observation difficult (Fig.4e and g). This problem was solved with the detachable device.


This work was supported in part by the Japan Society for the Promotion of Science (JSPS) KAKENHI Grant Number JP16H04170.


  1. Chueh, B.H., Huh, D., Kyrtsos, C.R., Houssin, T., Futai, N., Takayama, S. (2007). Leakage-free bonding of porous membranes into layered microfluidic array systems. Analytical Chemistry 79 (9), 3504–3508.
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A solvent-based method to fabricate PMMA microfluidic devices

Mustafa Al-Adhami; Abhay Andar; Elizabeth Tan; Govind Rao; Yordan Kostov*

Center for Advanced Sensor Technology, University of Maryland, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland, 21250.

*Email: kostov@umbc.edu

Why is this useful?

The demand for microfluidics has steadily increased, due in part to the growing popularity of point-of-care devices [1].  Often, microfluidic chips are fabricated in thermoplastics [1]. Thermoplastics are synthetic polymers that have gained popularity due to their ability to be molded into complex structures [3, 4]. They are often used as a safer and cheaper alternative to glass [3, 4]. However, proper sealing of these devices proves challenging, especially in the field of medical testing, where the demand for reliable devices is high. For example, pressure-sensitive adhesives, common sealants, can limit the size of microfluidic channels; some adhesive can exhibit reactive groups that interfere with analytical processes that run on the chip [5]. Hence, a method of sealing that is free from the aforementioned limitations is needed.

Here, a solvent-based method is presented. Polymethylmethacrylate (PMMA), a thermoplastic, exhibits softening at temperatures above its glass transition temperature (Tg) returning to its original state when cooled. This transition introduces several direct bonding options [6]. However, Tg of PMMA is 115 °C. The pressure required for bonding even at this temperature is fairly high. This can lead to imperfections in the channel dimensions, as the bulk of the material softens. The application of a weak solvent decreases Tg only for the surface of the plastic, thus reducing the required temperature and pressure for the process. The decreased pressure reduces the possibility of channel deformation. Furthermore, as the solvent-induced softening is limited only to the surface (the first few microns), the deeper channel structures are not affected. Hence, a direct solvent bonding method allows for an adhesive-free bonding and avoids a temperature-induced deformation. As a bonus, the mechanical properties of the bond are greatly enhanced [7]. It is worth noting that this approach is valid for microfluidic devices with channel depths greater than 100 microns, typically for devices produced by a direct laser etching.

Another advantage of this technique is that it results in the production of sterile devices when the weak solvent is ethanol. They can be manufactured quickly using basic equipment found in any laboratory [7]. To demonstrate this method, PMMA was used along with 90% ethanol as a solvent to bond to other sheet materials such as:

  • PMMA sheets,, to manufacture microfluidic mixers and other microfluidic devices for sample processing (Figure 1, a, d) [7];
  • ePTFE membranes, to make microfluidic de-bubblers (Figure 1, c); and,
  • Cellulose Acetate membranes, to make custom made dialysis devices (Figure 1, b).

Figure 1. A) Dialysis device B) Redox assay enclosure C) Microfluidic debubbler D) Microfluidic mixer

What do I need?


  • PMMA sheet, thickness of 1.5 mm (Astra Products)
  • PMMA sheet, thickness of 0.2 mm (Astra Products)
  • 10K, 20K MWCO Cellulose Acetate membranes (Thermo Fisher Scientific)
  • ePTFE membrane (Sterlitech,product number: PTU021350)
  • Metal vise (McMaster, product number: 5226A3)
  • 1000 grit Sandpaper (McMaster)
  • Silicone pad (McMaster)
  • KIM-WIPES (Kimberley Clark)
  • 2 rectangular metal sheets (McMaster)
  • Deionized water
  • 90% Ethanol (Decon Labratories, Fisher Scientific, Reagent grade)


  • CO2 Laser cutter (Universal laser systems)
  • Conventional toaster oven
  • Computer aided design (CAD) software (CorelDRAW X4)

What do I do?

  1. Design devise
    1. Draw the desired devise design using any available computer aided design (CAD) software.
    2. Export the CAD file into .dxf file format that is compatible with the laser cutter software.
  2. Laser cut design
    1. Place the PMMA sheet of 1.5 mm in thickness onto the bed of the laser cutter.
    2. Calibrate laser cutter according to sheet thickness.
    3. Select the correct laser setting in the laser cutter software. It should be height-aligned according to the material and thickness of the sheet.
    4. Laser cut the core pathway of the design onto the 1.5 mm thickness of PMMA.
    5. Next, place the other PMMA sheet of 0.2 mm in thickness onto the bed of the laser cutter and repeat points b-c
  3. Roughen the PMMA sheets
    1. After laser cutting, there should be a total of three pieces: core channel design (1) and cover sheets (2).
    2. Rinse the PMMA cutouts with deionized water and wet the sandpaper with tap water.
    3. Sand the wetted PMMA cutouts in a figure eight-like motion onto the wetted sandpaper until it is milky white. This is to ensure flat conformity on the PMMA sheets to increase bondage.
    4. Rinse PMMA cutouts with deionized water and dry using “KIM WIPES”.
  4. Bond the PMMA sheets
    1. Preheat the temperature-controlled oven to 55 °C. Place the metal vise and the rectangular metal sheets in the oven to preheat as well. Thermal gloves should be used for safety.
    2. Place a clean sheet of silicone onto a rectangular metal (aluminum) plate.
    3. Next, place the base cover of the microfluidic cassette on top of the silicone pad in a sandwich manner.
    4. Spray the 90% ethanol to the base cover sheet until all area is wetted.
    5. Place the core channel sheet of the PMMA cutout.
    6. Spray the 90% ethanol to the core channel sheet until the complete area, to be bonded, is wetted.
    7. Place the final cover sheet of the microfluidic cassette.
    8. Place the other silicone pad and the other rectangular metal sheet following it.
    9. Place the sandwiched PMMA sheet, silicone pad, and rectangular metal sheet in the metal vise carefully so it does not misalign the cassette (Figure 2.)
    10. Tighten the vise until can’t turn the lever anymore.
    11. Place the vise with the microfluidic cassette sandwich into the preheated oven for five minutes. This has to happen before the vise is cooled down.
    12. Allow to cool to room temperature and remove from metal vise and silicone pad.
    13. Add inlet and outlet fittings, either glue them on or place them depending on the method of preference
  5. Bonding PMMA to ePTFE(or cellulose acetate):
    1. Preheat the temperature-controlled oven to 85°C. Place the metal vise and the rectangular metal sheets in the oven to preheat as well. Thermal gloves should be used for safety.
    2. Place a clean sheet of silicone onto a rectangular metal (aluminum) plate.
    3. Next, place the membrane of the microfluidic cassette on top of the silicone pad in a sandwich manner.
    4. Spray the 90% ethanol on the membrane sheet until all area is wetted.
    5. Place the core channel sheet of the PMMA cutout.
    6. Spray the 90% ethanol to the core channel sheet until the complete area, to be bonded, is wetted.
    7. Place the final PMMA cover sheet of the microfluidic cassette.
    8. Place the other silicone pad and the other rectangular metal sheet following it.
    9. Place the sandwiched device, silicone pad, and rectangular metal sheet in the metal vise carefully so it does not misalign the cassette (Figure 2.)

      Figure 2. Bonding setup

    10. Tighten the vise until can’t turn the lever anymore.
    11. Place the vise with the microfluidic cassette sandwich into the preheated oven for five minutes. This has to happen before the vise is cooled down.
    12. Allow to cool to room temperature and remove from metal vise and silicone pad and remove the excess membrane if any with scissors.
    13. Add inlet and outlet fittings, either glue them on or place them depending on the method of preference

What else do I need to know?

In order to align the sheets on top of each other, three methods were used:

  1. For PMMA-PMMA devices it is enough to eyeball the alignment. The adhesion forces between the PMMA sheets with ethanol in between are enough to keep them fixed in place.
  2. An alignment manifold was also fabricated where the machined sheets are placed in. The manifold will prevent the movement of the sheets (Figure 3a.).
  3. Where the membrane is thick enough to drill a hole through, it is better to use three alignment pins. The pin holes are pre-fabricated when the device is machines. Toothpicks have been used as alignment pins (Figure 3b.).

    Figure 3. A) Alignment manifold B) 3 wooden pins are used to keep the layers from moving

  4. For thinner membranes, the machined PMMA is bonded on a slightly bigger membrane. The excess membrane is then removed with scissors.


This work was funded by DARPA, Biologically-derived Medicines on Demand (Bio-Mod) Project Grant (N66001-13-C-4023) for financial support.


  • Sia, S. K., & Kricka, L. J. (2008). Microfluidics and point-of-care testing. Lab on a Chip8(12), 1982. doi:10.1039/b817915h
  • Materials Used in Microfluidic Devices. (n.d.). SpringerReference. doi: 10.1007 /springerreference_67093
  • Liu, K., & Fan, Z. H. (2011). Thermoplastic microfluidic devices and their applications in protein and DNA analysis. The Analyst136(7), 1288. doi:10.1039/c0an00969
  • Tsao, C., & DeVoe, D. L. (2008). Bonding of thermoplastic polymer microfluidics. Microfluidics and Nanofluidics,6(1), 1-16.doi:10.1007/s10404-008-0361-x
  • Hong, T., Ju, W., Wu, M., Tai, C., Tsai, C., & Fu, L. (2010). Rapid prototyping of PMMA microfluidic chips utilizing a CO2 laser. Microfluidics and Nanofluidics9(6), 1125-1133. doi:10.1007/s10404-010-0633-0
  • Visakh, P. M., & Thomas, S. (2011). Engineering and Specialty Thermoplastics: Nylons: State of Art, New Challenges and Opportunities. Handbook of Engineering and Specialty Thermoplastics, 1-9. doi:10.1002/9781118229064.ch1
  • Al-Adhami, M., Tilahun, D., Gurramkonda, C., Rao, G., Kostov, Y (2016) Rapid detection of microbial contamination using a microfluidic devise. In: Biosensors and Biodetection: Methods and Protocols, Second Edition. Ed. A. Rasooly and B. Prickril. Springer.
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Manual Razor Patterned Tape Based Prototyping for Droplet Microfluidics

Saifullah Loneab* I. W. Cheongb and S. T. Thoroddsena

aDivision of physical Sciences and Engineering, King Abdullah University of Science & Technology, (KAUST), Thuwal, 23955-6900, Saudi Arabia.
bInstitute of Advanced Energy Technology, Kyungpook National University, Daegu, South Korea,
Phone: +821053165673, Office: +82-53-950-7590, FAX: +82-53-950-6594. Email: saifullah.lone@gmail.com, inwoocheong@gmail.com, and sigurdur.thoroddsen@kaust.edu.sa

Why is it Useful?

The subject of droplet microfluidics has grown in importance among researchers in chemistry, physics and biology, hence it has found applications in drug delivery, encapsulation, single-cell analysis, pickering-emulsion and phase-separation. For generating monodisperse droplets, various methods have been employed in constructing microfluidic devices. Emulsions with a coefficient of variation ≤ 5% have been previously reported in T-junction, flow focusing, co-axial, as well as other types of microfluidic devices. Microdroplets with ≤100 µm size offer attractive applications in industry and biology.  Small channel-diameters attained by clean-room soft lithography is the most precise technique for fabricating microfluidic devices.1, 2 This technique is widely used to make master molds for PDMS-based devices.3 However, regarding the cost and complexity, it is difficult to install clean-room soft lithography in financially challenged countries and laboratories. Therefore, the cost and special clean-room training restricts its wide-spread application. To develop low cost robust technologies; inkjet printing, controlled numerical machining, xurography or razor-writing, printed circuit technology, print-and-peel (PAP) microfabrication and 3-D printing have been tested to fabricate microfluidic devices without clean-room technology.  However, creating droplets under 100 µm size ranges by non-cleanroom technologies is challenging and open for upgradation. Recently, a rapid prototyping technique for microfluidics has been reported by employing laser-patterned tape4 This technique relies on computer-controlled CO2 laser beam. This work was further simplified by manual razor patterned tape-based prototyping for patterning mammalian cells.5 Building on this prototyping concept, we extended the idea to produce monodisperse droplets under 100 µm size rages by overlapping the razor patterned tape strips (at right angles) on a flat glass surface. The production of monodisperse emulsion under 100 µm size ranges are greatly useful in pharmaceutical and cosmetic industries. Hence, our approach may well serve as one of the simplest approaches to fabricate droplet microfluidic generators.

What do I need?   

  1. One-sided adhesive tape (Temflex 1500 electrical, thickness 150 µm)
  2. Flat glass slides, such as a microscope slide
  3. 30cm stainless steel metal ruler 
  4. Sharp razor blade
  5. Uncured mixture of PDMS base and curing agent (10:1 w/w)
  6. Oxygen plasma
  7. Oven or hot plate
  8. A microfluidic PDMS puncher for drilling holes
  9. Deionized water (D.I. water) and 20 cSt and 10 cSt silicone oil

What do I do?

Figure 1 outlines the prototyping procedure. Prototyping begins by attaching adhesive tape on a flat glass substrate. With a sharp razor-blade, the tape is cut into fine parallel strips. The thickness of the tape (150 µm) determines the depth of the microchannel, but this can be increased by attaching multiple layers of tape on top of each other. Next the tape is removed from the regions outside the fine strips.

To construct a cross-junction, one strip of the tape is lifted and horizontally placed on top of another at an angle of 90ᴼ. The junction is pressed gently to ensure the strips are well attached. These adhering strips of tape serve as a master for PDMS-based replica casting.

A mixture of PDMS silicone elastomer base and a curing agent (in 10:1 ratio) is poured on top of the master within a plastic petri dish. The mixture is degassed under vacuum for 1 h and cured for 4 hrs at 65°C. Cured PDMS replica is then cut and peeled-off from the master. The master can be used repeatedly to fabricate multiple copies of the PDMS replica by following the afore-mentioned steps. Inlet and outlet holes are drilled through PDMS replica, which is then bonded on a glass substrate, after both replica and glass has been exposed to oxygen plasma.  Figure 1(g) shows the resulting PDMS-device for generating monodisperse water-in-oil (W/O) emulsion. The technique is easily extended to fabricate T-junction or double T-junction prototypes (Figure 1h and i).

Figure 1. (a) Manual Razor Patterned Tape Based Prototyping for Droplet Microfluidics (b) Strips of adhesive tape on flat glass-substrate cut by a sharp razor-blade and a ruler, (c) The PDMS-casting, by pouring a mixture of PDMS silicone elastomer base and curing agent on top of the master in a plastic container. (d) Cut and peeled-off replica after curing. (e) Final assembled cross-junction microfluidic PDMS device. (f) Microfluidic device connected to syringe pumps under an optical microscope. (g)  Video frame showing water-in-oil droplet formation in a flow-focusing prototype. Panels (h) and (i) show razor patterned tape-based T-junction and double T-junction prototypes, respectively.
Figure 2. (a) Image sequence from a video recorded at 10 kfps showing water droplet formation at a cross-junction.  Time between subsequent frames is 200 µs.  (b) Droplet size as a function of capillary number based on the viscosity and flow-rate of the continuous-phase (20 cSt silicone oil), for the channel in panels (c) for 300 µm wide channel above the horizontal line and (d) for 150 µm channel below the horizontal line with 10 cSt silicone oil.  (c) Images extracted from video, showing flow regimes and droplet sizes as a function of flow-rate, with 300 µm channel width and 150 µm channel depth. (d) Video frame from smaller square channel with 150 µm width and depth.

Figure 2(a), demonstrates the droplet formation at a cross junction in our tape-based microfluidic device, with a channel width and depth of 300 µm and 150 µm respectively. In Figure 2(c), we kept the flow rate of aqueous phase fixed at 25 µl/min, while systematically increasing the flow-rate of outer continuous oil-phase (20 cSt silicone oil).  As the outer flow-rate is increased, the regime is found to shift from dripping at lower flow-rate to jetting at higher flow-rate (Figure 2(c)).  For lowest flow-rate, the aqueous-phase breaks into elongated plugs, while at higher flow-rates regular drops are pinched off.  Various factors affect the size of the droplets, but it is primarily determined by competition between viscous stress in the continuous phase Fv~ µU/d which tends to rip off the drop and the interfacial tension Fs ~ s/d which try to keep the drop attached. Here µ is the dynamic viscosity of the outer phase and U is its velocity; while s  is the interfacial tension between the water and the oil, s=0.040 N/m.  For small channels, the characteristic length-scale d is the same for the two forces and it therefore drops out of the balance and when Fv~ Fs then the non-dimensional capillary number Ca=µU/s characterizes their relative strength.  Figure 2b shows the droplet-size as a function of Ca.  When the flow-rate of oil-phase reaches 65 µl/min, the size of the droplets reaches ~100 µm and the droplet breakup occurs at a large distance from the cross-junction. Figure 2(d) shows drop formation with a channel width of 150 µm and a channel depth of 150 µm. In this case, the droplet size reaches down to ~73 µm, when the oil-phase (10 cSt) is flowing at 25 µl/min and aqueous-phase at 10 µl/min.


Acknowledgement: This work was jointly funded by King Abdullah university of Science & Technology (KAUST), Thuwal, Saudi Arabia , and the Ministry of Trade, Industry and Energy, Korea (Grants No. 10067082 and 10070241).



[1] Qin, D.; Xia, Y.; Whitesides, G. M. Rapid prototyping of complex structures with feature sizes larger than 20 μm. Adv. Mater. 1996, 8, 917-919.

[2] Xia, Y.; Whitesides, G. M. Soft Lithography. Angew. Chem. Int. Ed. 1998, 37 550- 575.

[3] Duffy, D. C.; McDonald, J. C.; Schueller, O. J.; Whitesides, G. M. Rapid Prototyping of Microfluidic Systems in Poly (dimethyl siloxane). Anal. Chem., 199870, 4974–4984.

[4] Luo, L. W.; Teo, C. Y T.; Ong, W. L.; Tang, K. C.; Cheow, L. F.; Yobas, L. Rapid prototyping of microfluidic systems using a laser-patterned tape J. Micromech. Microeng. 2007, 17 N107–N111

[5] Anil, B. S.; Ali, H.; Cheul, H. C.; and Raquel, P-C. Adhesive-tape soft lithography for patterning mammalian cells: application to wound-healing assays. BioTechniques, 2012, 53 315–318.

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Rapid Inoculation and Recovery of Microbes in a Microfluidic Device

Greiner, A.1,2, Tekwa, E.W.1,3, Gonzalez, A.1, Nguyen, D.4

1Department of Biology, McGill University, 1205 Dr. Penfield, Montreal, QC, H3A 1B1, Canada.
2Department of Ecology and Evolution, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
3Department of Ecology, Evolution, and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ, 08901, USA.
4Meakins Christie Laboratories, Research Institute of the McGill University Health Centre, and Department of Medicine, McGill University, 1001 Decarie Blvd, Montreal, QC, H4A 3J1, Canada.


Why is this useful?

Microfluidic devices are used for many different types of experiments across the medical, ecological and evolutionary disciplines (Park et al., 2003; Keymer et al., 2008; Connell et al., 2013; Hol & Dekker, 2014). For example, microfluidic devices for microbial experiments require inoculation into smaller chambers that simulate natural microbial environments such as porous soils (Or et al., 2007) and biological hosts (Folkesson et al., 2012). These devices often involve complicated pump setups and irreversible seals. We developed a technique that requires only common lab equipment and makes the device reusable while also allowing the microbes to grow undisturbed (based on Tekwa et al., 2015; Tekwa et al., in review). Here, we provide a detailed guide for the assembly and the previously undocumented non-destructive disassembly of polydimethylsiloxane (PDMS) experimental devices to recover microbes in situ, which can then be plated for relative counts and further molecular analyses of population changes. This is complemented by videos for each step.

Figure 1: Microfluidic device containing 14 habitats on an elastomer (PDMS) layer pressed onto a 60mm x 24mm glass cover slip. The habitats are 10 or 20µm in depth, range from 1400 µm to 2670 µm in diameter and take the shape of a ring or network of patches. This device is used to test the effects of habitat patchiness on microbe dynamics. Habitats were dyed blue for visualization. For more information see Tekwa et al. (2015).


What do I need?

  • Single-layer PDMS devices with habitats on one side
  • Pipette + sterile pipette tips
  • Sterile petri dishes (1/device)
  • Sterile tweezers
  • Inoculum
  • Filtered water
  • Kimwipes
  • Autoclavable plastic container
  • Ethanol
  • Tinfoil
  • Sterile 1μL inoculating loop (1/habitat)
  • Sterile eppendorfs
  • Phosphate-buffered saline (PBS)
  • Biological safety cabinet (BSC)

How do I do it?

  1. Clean the PDMS devices: The PDMS device should be pre-treated once with 0.01N HCl for one hour and plasma-treated to keep it hydrophilic and amenable to bonding to glass or plastic substrates (Cho et al., 2007; Tekwa et al., 2015). Fill autoclavable plastic container 1/3rd full of 70% ethanol and PDMS devices and then cover with tinfoil, let them sit in this for >30 minutes before carefully disposing of the ethanol down the sink. Fill and empty the container with water 10 times in order to rinse the devices. Lastly, fill the container with filtered water, seal with tin foil and autoclave in order to sterilize the devices.
  2. Inoculating the devices (perform in a Biological Safety Cabinet, BSC): Set the devices to dry in the BSC for 30 minutes. Place the devices with features facing up on the lid of a petri dish and place a small amount (i.e. 0.7 µL) of inoculum onto each (of 14 in sample device Fig. 1) habitat. The amount of liquid must be sufficient to fill the habitats, but not too much as to prevent bonding between PDMS and the cover glass/petri dish (Fig. 2). Using sterile tweezers, pick up the device and place face down into the centre of a petri dish or cover glass, sealing it to the surface by pushing on the back with gloved fingers repeatedly, using a kimwipe to wick excess liquid away from the side. Then surround, but not touch, the device with kimwipes soaked in filtered water (Fig. 3) to ensure that the device does not dry out in the incubator, before closing the petri dish. Place upright in incubator for the desired amount of time. The experiment can now proceed untouched for up to 24 hours (see Supplementary video).

Figure 2. Device with bacteria droplets, 1 droplet per habitat.

Figure 3. An ‘upright’ petri dish + kimwipes + device + coverslip ready to be incubated.


  1. Recovering from the devices (perform in a BSC): Open petri dish, carefully remove and discard kimwipes and then use sterile tweezers to gently unseal the device and place face up in the lid of the petri dish. By around 12 hours, the spaces between the habitats will be void of liquid from PDMS absorption, preventing microbes from being mixed across chambers during disassembly. Habitats that have dried out will appear white (Fig. 4) and cannot be used.  Dip sterile inoculating loop into an eppendorf with PBS, then use that loop to scrape one of the habitats (Fig. 5).  Dip that inoculating loop back into the eppendorf media again, which can then be grown overnight for further analyses such as plating for relative cell count (if there are different strains) and other molecular analyses. Repeat for the rest of the habitats that you are interested in, using new inoculating loops. The PDMS device can now be cleaned as in Step 1 and reused again.

Figure 4. View of an inoculated and incubated device, looking through the bottom of a petri dish.


Figure 5. Recovering bacteria from a habitat in the disassembled PDMS device.


What else should I know?

The recovery technique can be used to estimate relative proportions of different types of microbes (e.g. morph frequencies) which is useful when performing competition assays and evolutionary experiments. Unlike in Tekwa et al. (2015), this technique forgoes the use of a confocal microscope; assessment of the contents of the device is instead performed through direct microbe recovery and standard plating procedures.


Links to Videos

These videos go through the specific procedure that we used to perform experiments on competition and cooperation in Pseudomonas aeruginosa and may be useful in determining specific amounts of media, growth times, etc. that may be utilized for experiments with similar PDMS microfluidic devices.

Part 1 – Intro + Washing the Devices https://youtu.be/Bne3ZN3wU4Q

Part 2 – Inoculating the Devices https://youtu.be/p-UYIRreYyM

Part 3 – Recovering from the Devices https://youtu.be/YLnmGxqMYgE

Supplementary – Fluorescent Bacteria Experiment https://youtu.be/lgMtryS62pA



AGr was supported by an NSERC Undergraduate Student Research Award and by an NSERC Discovery Grant. EWT was supported by the Fonds Québécois de la Recherche sur la Nature et les Technologies and the Québec Centre for Biodiversity Science. AGo was supported by the Canada Research Chair program and NSERC Discovery grants. DN was supported by a CFI Leaders Opportunity Fund (25636), a Burroughs Wellcome Fund CAMS award (1006827.01) and a CIHR salary award.



Cho, H., Jönsson, H., Campbell, K., Melke, P., Williams, J. W., Jedynak, B., … & Levchenko, A. (2007). Self-organization in high-density bacterial colonies: efficient crowd control. PLoS biology, 5(11), e302.

Connell, J. L., Ritschdorff, E. T., Whiteley, M., & Shear, J. B. (2013). 3D printing of microscopic bacterial communities. Proceedings of the National Academy of Sciences, 110(46), 18380-18385.

Folkesson, A., Jelsbak, L., Yang, L., Johansen, H. K., Ciofu, O., Høiby, N., & Molin, S. (2012). Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective. Nature reviews. Microbiology, 10(12), 841.

Hol, F. J., & Dekker, C. (2014). Zooming in to see the bigger picture: Microfluidic and nanofabrication tools to study bacteria. Science, 346(6208), 1251821.

Keymer, J. E., Galajda, P., Lambert, G., Liao, D., & Austin, R. H. (2008). Computation of mutual fitness by competing bacteria. Proceedings of the National Academy of Sciences, 105(51), 20269-20273.

Or, D., Smets, B. F., Wraith, J. M., Dechesne, A., Friedman, S. P. (2007). Physical constraints affecting bacterial habitats and activity in unsaturated porous media – a review. Advances in Water Resources, 30(6), 1505-1527.

Park, S., Wolanin, P. M., Yuzbashyan, E. A., Silberzan, P., Stock, J. B., & Austin, R. H. (2003). Motion to form a quorum. Science, 301(5630), 188-188.

Tekwa, E. W., Nguyen, D., Juncker, D., Loreau, M., & Gonzalez, A. (2015). Patchiness in a microhabitat chip affects evolutionary dynamics of bacterial cooperation. Lab on a Chip, 15(18), 3723-3729.

Tekwa, E.W., Nguyen, D., Loreau, M., Gonzalez, A. Defector clustering is linked to cooperation in a pathogenic bacterium. In review.

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Rapid and easy fabrication of glass-bottom culture dishes for long-term live cell imaging

Ayako Yamada123, Jean-Louis Viovy123, Catherine Villard123 and Stéphanie Descroix123

1 Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France.

2 Sorbonne Universités, UMPC Univ. Paris 06, Paris, France

3 Institut Pierre-Gilles de Gennes, Paris, France

Email: ayako.yamada@curie.fr


Why is this useful?

Glass is a versatile surface for chemical treatments, and it still is by far the most used substrate for surface engineering (e.g. micropatterning, surface chemistry) or plasma-bonding of PDMS microfluidic devices. For cell culture on such substrates, glass-bottom culture dishes are desired to keep over the cells well defined medium volumes, and to protect the cells from contamination and medium evaporation. Moreover, they are optically better suited for microscopy observation than polystyrene dishes routinely used for cell culture. Although glass-bottom culture dishes are commercially available (e.g. Fluorodish from WPI), the presence of plastic walls limits the treatments that can be performed onto the glass bottom surface and those are more expensive ( 5 € per dish; φ 50 mm) than polystyrene dishes (e.g. φ 40 mm dish from TPP, 0.5 € per dish). In this Tip, we describe an easier way than a previous Tip1 to transform a polystyrene culture dish into a glass-bottom one, while preserving the possibility to apply to the glass any treatment before its assembly into a dish. Note that in this method, the body of the culture dish will be upside down and the lid is thus no longer lifted above the dish opening by lid stoppers. However, the gas exchange through the gap between the body and its lid seems to be enough to culture cells healthily in this dish. In summary, this Tip provides a low-cost and rapid solution for cell culture in a microfluidic device or on an engineered surface directly in a culture dish, suited for a long-term live cell imaging.


What do I need?      

  • φ 40 mm polystyrene tissue culture dish (e.g. TPP #93040)
  • φ 40 mm cover slide (e.g. Thermo Fisher Scientific #11757065, ∼0.2 € per slide)
  • Large screw driver (or a similar tool)
  • Uncured mixture of PDMS base and curing agent (10:1 w/w)
  • Oven or hotplate
  • Ferromagnetic metal plate (e.g. lid of a PDMS container, optional)
  • Cylindrical magnets (optional)


What do I do?

  1. Place a polystyrene culture dish upside down on a surface and hit a few times the center of the dish bottom with the grip of a large screw driver (Fig. 1a) until the dish bottom falls apart from the dish wall (Fig. 1b). The bottom should fall easily with the success rate around 9 over 10. Avoid breaking the dish wall by hitting the bottom too strongly.
  2. Spread uncured PDMS mixture on a flat substrate (e.g. a larger plastic Petri dish) and coat the edge of the dish (broken part up) with PDMS (Fig. 1c).
  3. Place the dish (broken part up) on a cover glass slide (Fig. 1d) and cure PDMS in an oven or on a hotplate e.g. at 80 °C for 10 min (Fig. 1e).
  4. Surface treatment (e.g. micro-contact printing) or plasma-bonding of a PDMS chip to the glass surface can be performed after or before the dish assembly (Fig. 1f).

  1. To keep humidity for on-chip cell culture, the dish can be filled with e.g. phosphate buffered saline (Fig. 2a). Dishes with chips or micropatterns loaded with cells can be placed in a CO2 incubator with or without further protection (Fig. 2b).
  2. Long-term live cell imaging can be performed using a stage top incubator (Fig. 2c).


What else should I know?

  1. Depending on the support type of microscopes, it might be necessary to well align the contours of the dish and the glass slide. This can be done using cylindrical magnets (3 per dish) and a ferromagnetic metal plate (Fig. 3a) during PDMS curing in an oven or on a hotplate (Fig. 3b).




This work is supported by the French National Research Agency (ANR) as part of the “Investissements d’Avenir” program (reference: ANR 10-NANO 0207) and ERC Advanced Grant CellO (FP7-IDEAS-ERC-321107).



[1] Caballero D, Samitier J, Different strategies for the fabrication of cell culture chambers for live-cell imaging studies. Chips and Tips, 02 Dec 2014 (https://blogs.rsc.org/chipsandtips/2014/12/02/different-strategies-for-the-fabrication-of-cell-culture-chambers-for-live-cell-imaging-studies/)



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Multilayer photolithography with manual photomask alignment

Frank Benesch-Lee, Jose M. Lazaro Guevara, and Dirk R. Albrecht

Worcester Polytechnic Institute, Worcester, MA 01609 USA

Why is it useful?

Modern microfluidic devices can incorporate channels of different heights to fulfill their designed function. Examples include hydrodynamic focusing [1], cell traps [2], and chambers that isolate cellular components [3]. These devices are fabricated from a multilayer SU-8 photoresist master mold. Each layer height requires a separate set of photolithographic steps, including photoresist spin, photomask alignment, exposure, and bakes, followed by a development step at the end to reveal the 3D resist pattern.

Mask aligners have microscopes and stage micrometers for precise, micron-scale alignment of each layer’s photomask with visible marks on the substrate wafer.  They are indispensable tools for creating multilayer patterns with accurate registration, but while available in cleanrooms at many research universities, their substantial expense may place them out of reach of teaching institutions and individual laboratories.

In contrast, single-layer microfluidics can be prepared using an inexpensive UV light source, or even a self-made one [4]. In principle, manual photomask alignment could be made under a microscope, then brought to the UV source, yet this poses several complications. First, alignment features can be very difficult to see using inexpensive microscopes or stereoscopes, especially in thin SU8 layers, due to poor contrast between exposed and unexposed regions before development. Second, misalignment can occur during movement to the exposure system.

Here we present a manual photomask positioning method that yields a 50 µm accuracy, without the aid of a mask aligner.


What do I need?

  • Equipment and supplies for photolithography:
    • Spin coater, and UV exposure system
    • Substrate wafer and SU-8 photoresist
  • Small microscope (e.g. USB) or stereo microscope
  • Photomask transparencies for each layer
  • Scotch tape
  • Fine-tip permanent marker
  • Straight razor blade
  • Cutting mat
  • 4 small (3/4”) or mini (1/2”) binder clips
  • Glass plate, approx. 4 x 5”, compatible with exposure system


What do I do?

  • Cut the photomasks from the transparency sheet, leaving 4 corner tabs. Align the two masks relative to each other under the microscope (Figure 1a) and clip them together with a binder clip. Ensure correct mask orientation and check alignment accuracy at multiple alignment marks across the mask. (Note that horizontal alignment accuracy with a stereomicroscope is low, because each eye’s optical path is angled 5 – 8 degrees, whereas vertical alignment is unaffected. Align in the vertical direction first then rotate the masks 90 degrees to ensure accurate alignment in both horizontal and vertical directions.) Add binder clips to each corner (Figure 1b), and verify alignment. Next, remove one binder clip at a time and use a straight razor blade to cut a sharp V-notch into each tab, through both masks. Press the blade straight down to avoid shifting the alignment. Replace the binder clip, and proceed to the next corner until all 4 notches are cut (Figure 1c).





  1. Spin the first layer of SU-8 onto the wafer to the desired thickness and prebake. Attach 4 pieces of scotch tape onto the bottom of the wafer so that the sticky side faces up (Figure 2a). Position the first mask on the wafer, pressing gently to adhere it to the tape tabs. Use a fine-tip marker to trace the alignment notches (Figure 2b) onto the scotch tape (Figure 2c).  Transfer to the UV exposure system and expose.  Carefully remove the mask without detaching the scotch tape from the wafer and postbake.  Scotch tape is compatible with 95 °C baking.  Apply an additional piece of tape to cover the sticky tape tabs to protect the marker from smearing and allow smooth alignment of the next mask.




  1. Spin coat the next photoresist layer and prebake (Figure 3a). Mount the wafer onto a glass plate with a loop of scotch tape to keep it in place. Position the second mask onto the wafer, ensuring that alignment “V” markings are centered within each alignment notch and across all 4 corners (Figure 3b). Affix the mask to the glass plate with thin (2-3 mm wide) pieces of tape, and adjust alignment as necessary.  Carefully transfer the glass plate with wafer and aligned photomask for exposure (Figure 3c).



  1. Repeat step 3 for any additional layers. Remove the tape tabs and develop the photoresist. Evaluate alignment accuracy under a microscope (Figure 4).




In this tip, we present a method for manual alignment of multiple transparency photomasks.  We achieved repeatable accuracy of <100 µm and as good as 50 µm (Figure 4a). These accuracies are within required tolerances of many multilayer designs (Figure 4b).  In many cases, minor design alternatives can relax alignment tolerances, such as in a trap design containing a thin horizontal channel that allows fluid bypass but captures larger objects (Figure 4c). In this example, a 100 µm wide bypass channel only partially covered the trap indentations, whereas widening the bypass channel to 400 µm enabled a functional device despite slight misalignment.  Overall, this simple method allows fabrication of microfluidic device molds containing multiple layer heights, without expensive mask alignment equipment, to an accuracy of at least 50 µm.  Furthermore, after alignment marks are cut, no microscope is needed at all during the photolithography process, speeding the fabrication of multiple masters.


Funding provided by NSF IGERT DGE 1144804 (FBL), Fulbright LASPAU (JMLG), University of San Carlos of Guatemala (JMLG), NSF CBET 1605679 (DRA), NIH R01DC016058 (DRA), and Burroughs Wellcome CASI (DRA).Acknowledgments:



  1. Chih-Chang, C., H. Zhi-Xiong, and Y. Ruey-Jen, Three-dimensional hydrodynamic focusing in two-layer polydimethylsiloxane (PDMS) microchannels. Journal of Micromechanics and Microengineering, 2007. 17(8): p. 1479.
  2. Erickson, J., et al., Caged neuron MEA: A system for long-term investigation of cultured neural network connectivity. Journal of Neuroscience Methods, 2008. 175(1): p. 1-16.
  3. Taylor, A. M., et al., A microfluidic culture platform for CNS axonal injury, regeneration and transport. Nature Methods, 2005. 2(8): p. 599-605.
  4. Erickstad, M., E. Gutierrez, and A. Groisman, A low-cost low-maintenance ultraviolet lithography light source based on light-emitting diodes. Lab on a Chip, 2015. 15(1): p. 57-61.


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