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FAQ: µ-Slides and µ-Dishes


What are the µ-Slides’ dimensions?

Please refer to the µ-Slide product section of our website where dimensions for all slides are provided.

Dimensions of basis µ-Slide (w x l x h):

25.5 mm x 75.5 mm x 1.5 mm


What are the microscopy properties of the ibidi Standard Bottom (µ-Slides, µ-Dishes, µ-Plates)?

The µ-Slides and µ-Dishes are optimized for inverted microscopes. The ibidi Standard Bottom matches the No 1.5 coverslip thickness (180 µm), and is made from high-quality plastic material. Autofluorescence, birefringence, and the refractive index of the ibidi Standard Bottom are similar to those of glass, allowing for the use of all kinds of objective lenses (up to 100x oil immersion). The slide optics is designed to be used with 0.17 mm corrected objective lenses.


Thickness

The thickness of the coverslip is a crucial aspect of imaging quality. The typical thickness of a coverslip is 0.17 mm (170 µm, No. 1.5). Most objective lenses for microscopy are made for this special thickness. Thinner or thicker substrates require correction collars on the objective lenses, and that prevents the formation of blurred images by spherical and chromatic aberrations.

Thickness of standard glass coverslips:

No.

Thickness

No. 0

0.08 - 0.12 mm

No. 1.0

0.13 - 0.16 mm

No. 1.5 

0.16 - 0.19 mm

No. 2.0

0.19 - 0.23 mm

(Source: Gerhard Menzel, Glasbearbeitungswerk GmbH & Co. KG, Braunschweig, Germany)

Thickness of ibidi bottom materials:

The ibidi bottom materials provide a standard No. 1.5 thickness with a very low variation (selected quality).   

Material

Thickness

Refractive
index
(nD 589 nm)

Auto-
fluorescence

Abbe
number

ibidi Standard Bottom

No. 1.5, 180 µm (+/- 5 µm)

1.52

very low

56

ibidi glass bottom

No. 1.5, 170 µm (+/- 10 µm)

1.52

very low

55

standard glass coverslip

No. 1.5, 175 µm (+/- 15 µm)

1.52

very low

55


Refractive Index

The refractive index of the ibidi Standard Bottom is identical to that of glass coverslips and immersion oil. This leads to perfect, high-resolution microscopy, especially in combination with immersion oil.


Abbe Number / Material Dispersion

The Abbe number is a measure for material dispersion, and is defined as the variation of the refractive index with different wavelengths. Therefore, the dispersion is a measure for chromatic aberrations. The Abbe number summarizes the dispersion into one value. It is calculated from the refractive indices at three different wavelengths. The higher the Abbe number, the better the optical quality for microscopy. A material with an Abbe number larger than 55 is considered to be well-suited for high-resolution microscopy. The ibidi Standard Bottom has an Abbe number of 56.


Birefringence

The birefringence of both the ibidi Standard Bottom and the ibidi Glass Bottom  is very low, and this allows for the use of differential interference contrast (DIC) microscopy. The special ibidi channels slides are not compatible with DIC, however, since the channel’s ceiling has a high birefringence. The µ-Slides’ lids are also problematic in combination with DIC. For the latter problem, and also for the open well formats (e.g., µ-Dishes 35 mm), we provide a special DIC Lid, with a glass coverslip inside the lid. This allows you to use DIC with uncompromised quality.


Autofluorescence

Unlike all other plastic materials for cell culture, the ibidi Standard Bottom provides an excellent signal-to-noise-ratio, similar to glass. Please test this tremendous optical quality with a free sample.


How does the µ-Slide’s optical quality compare to that of glass?

The polymer from which ibidi's µ-Slides are produced has almost the same optical quality as glass. The following PDF provides a comparison between the autofluorescence signal from CCD camera noise, a µ-Slide and a coverslip. In addition, some commonly used plastic materials, like those used in petri dishes, are compared.
>> Download PDF


Are the µ-Slides biocompatible?

The µ-Slides and µ-Dishes are made of biocompatible materials. The biocompatibility of all types of ibidi µ-Slides and µ-Dishes conform to the EN ISO 10993-5 standard (Test for cytotoxicity: in vitro methods).


What is the ibiTreat surface?

ibiTreat is a physical surface modification that provides improved cell adhesion on µ-Slides. The surface is comparable to standard cell culture flasks and Petri dishes. The adhesion of cells to ibiTreat µ-Slides is strong enough to perform flow experiments simulating the physiological shear stress of blood flow. The surface has been tested with over 20 different cell lines and primary cells, with positive results.


Which surface coatings are offered by ibidi?

The growth, development, and signaling of cells cultured on surfaces strongly depend on the adhesion factors and surface modifications with which the cell culture labware is coated/treated. One of the advantages of the ibidi µ-Slides is that these can be treated similarly to standard plastic labware.

For standard cell culture applications, ibidi offers µ-Slides with the following approved surfaces.

Tissue culture treated surface – ibiTreat
ibiTreat is a physical surface modification that provides improved cell adhesion on µ-Slides. The surface is comparable to the surface of standard cell culture flasks and Petri dishes. The adhesion of cells to ibiTreat µ-Slides is strong enough to perform flow experiments simulating the physiological shear stress of blood flow. This surface has been tested with over 20 different cell lines and primary cells, with positive results.

Collagen IV
Collagen type IV is the type of collagen found primarily in large extracellular basement membrane structures and complex organs. Collagen IV substrates have been tested on a variety of standard cell lines, such as epithelial, endothelial, nerve, and muscle cells. ibidi µ-Slides are coated with a mouse Collagen IV.

Poly-L-Lysine (PLL) / Poly-D-Lysine (PDL)
PLL and PDL are polymers of the amino acids L-Lysine and D-Lysine respectively. Poly-Lysine is one of the most commonly used adhesion substrates. It is suitable for use with a large variety of cell types, especially for neuronal cultures. Adhesion, using this polymer, is mediated by an integrin-independent mechanism.

Fibronectin
Fibronectin is a glycoprotein that is widely used in cell culture coatings. It plays an important role in cell surface interactions, which are mediated by an RGD motive. Fibronectin allows neurite outgrowth, and has been used for glial and neural cells.

Due to its short shelf life, Fibronectin coated µ-Slides are available only on request. Delivery time is estimated at three weeks. Please contact us for further information.

Hydrophobic, uncoated
An uncoated surface does not permits direct cell growth. Due to its hydrophobicity, it can be used for specific coating procedures or for non adherent cells. This bottom material is a hydrophobic version of the ibidi Standard Bottom, and has identical optical properties.

For detailed information on coating procedures please refer to ibidi’s Application Note 08 "Cell Culture Coating".


Do cells directly grow on the ESS surface?

No, the ESS surface needs to be coated before cells can be seeded. A freshly made protein coating (e.g., of Fibronectin or Collagen) works well in promoting cell attachment.

Please refer to Application Note 08 "Cell Culture Coating" for a coating protocol.


Which materials are compatible with µ-Slides?

Hydrogenperoxide, Sodium hydroxide, Sulfuric acid

+++

DMSO, Acetonitrile

+++

Acetone, Methanol, Ethanol, Isopropanol

+++

Formaldehyde

+++

Ethyl acetate

++


Pentane, Heptane, Hexane

---

Oleic acid

---

Toluene, Benzene

---

Pyridine / Lutidin

---

THF, Chloroform

---

Modeling clay / Plasticine

---

Mineral oil

---


My µ-Slides show scratches on the bottom. Where do these come from, and how can I prevent them?

The ibidi Standard Bottom is very sensitive to mechanical scratching. If you do not use extra caution when placing the ibidi µ-Slide directly on the bench, or inside the incubator, it is likely to be harmed. As a result, small scratches could be microscopically visible. To avoid this effect, we recommend protecting the bottom material by using, for example, a µ-Slide Rack. This solution also allows for convenient handling of several µ-Slides at once.


What is your recommendation with regards to reusing μ–Slides?

We do not recommend reusing the slides as one might experience problems with protein remains, sterility, washing, drying, and more.


How do I properly fill the µ-Slide 2 Well Ph+ or the µ-Slide 4 Well Ph+?

The Ph+ versions are easily filled by using a normal pipette. There are special openings near the edges that allow easy access to the liquid in the well. Filling and medium exchange can be done without the fear of creating air bubbles. Due to the geometry, air bubbles cannot be trapped when the correct well volume is used. Please find a detailed description in the Instructions.

 


What does Ph+ in the µ-Slide 2 Well Ph+ or the µ-Slide 4 Well Ph+ stand for?

Ph stands for phase contrast. The Ph+ versions of the µ-Slide 2 Well and µ-Slide 4 Well are specially designed for excellent phase contrast microscopy. Working with the Ph+ versions diminishes the meniscus effect, so that satisfying phase contrast microscopy is possible over the entire well.


Is the µ-Slide III 3in1 controllable by the ibidi Pump System?

Yes.  With a special setup, the µ-Slide III 3in1 can be fully controlled with the ibidi Pump System. In this manner, adherent cells in the slide can be exposed to alternating gradients using laminar flow.


Is it possible to work with Matrigel™ in a µ-Slide 2 x 9 Well?

Yes. You can for example embed a cell spheroid into the gel and cast it into the center well of the µ-Slide 2 x 9 Well. It is also possible to fill the minor wells with Matrigel and seed cells on top.
For detailed information, please refer to our Application Note Co-Cultivation (AN 10).


Can cells move across the small barriers between the wells in a µ-Slide 2 x 9 Well?

Yes. Over time motile cells can move or proliferate over the barriers in a µ-Slide 2 x 9 Well, especially when they are seeded at high confluence. To avoid this, it may be helpful to coat the surface of the slide.


Is it possible to perform independent experiments in the minor wells of a µ-Slide 2 x 9 Well?

No, as there is a high chance of cross contamination between the minor wells of the µ-Slide 2 x 9 Well. However, two independent experiments can be performed in the two major wells.


Which mounting medium is recommended for mounting glass slides and coverslips in a 12 Well Chamber, removable?

All common mounting media can be used in a 12 Well Chamber, removable, whether they are aqueous or non-aqueous. However, ensure that the product chosen is suitable for the staining technique to be employed.


Can the ibidi Mounting Medium be used with a 12 Well Chamber, removable?

Yes, it can be used with a 12 Well Chamber, removable. But keep in mind that the ibidi Mounting Medium is non-drying and therefore will not glue the coverslip to the glass slide.


Is the silicon gasket of a 12 Well Chamber, removable, reusable?

Reusing the silicon gasket of a 12 Well Chamber, removable is not recommended as ibidi only guarantees the product’s adhesive capacity for a single use.


How long can cells be cultured in the µ-Slide 18 Well - Flat?

Due to the open well structure of the µ-Slide 18 Well – Flat and the low volume of substances being used, evaporation rates are fairly high. Therefore, the slide is only recommended for use with short term assays, i.e. assays that do not exceed 48 hours.


Is the flat design of the µ-Slide 18 Well – Flat also compatible with upright microscopes?

The µ-Slide 18 Well – Flat was originally designed only for inverted microscopes. Nevertheless, it is possible to use the slide with upright microscopes if the microscope’s objectives have working distances of 2 mm or more. Alternatively, water dipping objectives may be used. Water dipping lenses are designed to be used with upright microscopes, and slides without coverslips, by dipping them directly into an open cell culture well. Please contact your microscope supplier for such lenses.


Can the sticky-Slide be detached from its substrate mounting?

All sticky-Slides make a tight seal that is not easily broken with mechanical forces. Acetone can be used (e.g., by immersing the slide in a beaker of Acetone) to detach the slide from its mounting. Keep in mind, however, that Acetone may be incompatible with your surface or substrate.


Which is the optimal mounting solution for immunofluorescence?

We recommend ibidi Mounting Medium, a glycerol-based mounting solution optimized for ibidi µ-Slides, µ-Dishes, µ-Plates, and both adherent cells and tissue sections that are immunofluorescent stained. It contains an inhibitor that retards photobleaching of fluorochromes. The ibidi Mounting Medium is a ready–to–use solution.


How can evaporation be prevented?

It is true that small volumes of medium can evaporate quickly, depending on incubating conditions, and especially during long term experiments. Also, all cell culture incubators need a fairly long time to recover humidity, particularly after door openings. While temperature and CO2 recover within minutes, full humidity recovery can take hours.

Due to these issues, we recommend the following techniques for controlling and decreasing evaporation:

1. Pack a Petri dish with wet tissues

2. Use a humidifying chamber (Olaf)

3. Cover the slide with Parafilm

4. Use ibidi Anti-Evaporation Oil (Silicone oil).

Detailed protocols and recommendations can be found in our Application Note Co-Cultivation (AN 10).


Which immersion oils are compatible with ibidi products?

Company

Product

Ordering Number

ibidi

Immersion Oil

(ibidi) 50101

Zeiss

Immersol 518 F

(Zeiss) 444960

Zeiss

ImmersolW 2010

(Zeiss) 444969

Leica

Immersion liquid

(Leica) 11513859


How do I prepare a 3D gel using the collagen solution that you provide?

The collagen forms a firm and clear gel when brought to neutral pH at room temperature or 37°C. We provide detailed 3D protocols here.


My gel looks very inhomogeneous. What is the reason for that?

Normally, this is caused by the start of polymerization, which is due to insufficient cooling. Incomplete mixing can also cause this phenomenon. The solution to this problem is to either cool the reagents you are using more completely, or to mix the viscous collagen solution more thoroughly.