New user project questions

Thanks for contacting us about using the microscope systems and other facilities we offer.

Since you are a new user, we will need to work with you a little in order to help you select appropriate microscope systems, figure out sample preparation and work out optimal imaging hardware settings.

Our aim is to work with you to find the best and/or most sensible way to get the image Information you need. We will use the info you give us below when we discuss your imaging project with you one on one. It will help us all get going much faster!

Please come to our upcoming meeting having already thought about answers to the following questions. You might even want to discuss these specific point with your adviser / supervisor. (if you want you can also send the answers to lmf@mpi-cbg.de ... but its not supposed to be yet another form to fill in, rather, en exercise to get you thinking about what you really want to do, and get it done faster and better!)

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First we have to start with your "Experimental Hypothesis": Please try to explain to us the following:

1) What is your experimental hypothesis?

2) How you will test it - what info do you need?

3) how will you get that info - what will you measure ?

4) ...and how will you analyze the info you get in order to prove your hypothesis right or wrong?

5) What controls will you need?

6) What statistical test will you use to test your hypothesis?

7) Are you interested in colocalization analysis?

All these affect the way the images are best collected: on what kind of microscope and with what hardware settings / objective lens etc.

The laser scanning confocal microscope is very useful, but its not the only tool we have! Don't be afraid to open the toolbox and see what microscopes are inside...

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Second, we can talk about "Sample Preparation, Dyes and Mounting" The answers to the questions in the Experimental Hypothesis" section will help determine some of the answers here:

1) What is the sample? Organism? Tissue? Cell Type? Living? Fixed?

2) How is it prepared? Grown on glass? Tissue section? Living Embryo?

3) How is it mounted? Under a (proper exactly 0.17 mm) coverglass? Underwater in an agarose well? In an agarose column? On a filter/carrier/special chamber?

4) What Staining / Dyes / contrast agents will you use? Fluorescence and/or transmitted light? Electron beams?

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The third task is to use the answers from parts 1 and 2 to select appropriate microscope systems which will be able to get the information you need out of your samples in a sensible and efficient way.

If the only tool you have is a hammer - every problem begins to resemble a nail.

We have a large toolbox of different kinds of microscopes ... lets take a look inside!

1) Do you need 2D (single focal plane) or 3D images (z stacks)?

2) Do you need time series? If so, what time resolution / frames per seconds do you need?

3) Do you need high Signal : Noise (see the difference in intensity accurately), or will somewhat noisy images work for you (just see where stuff probably is)

4) What is the size of the field of view that you need?

5) How big are the objects you are interested in? What (optical) resolution do you need (what should the pixel spacing at the sample be)? 5 nm? 200 nm? 1 micro meter? Bigger? (Hint: Theory says you need no more than 2.3-3 pixels across the object of interest in order to image it properly)

cheers your imaging facility team