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[CL] OK, I'll pick up the suggestion of Steffen and start using the wiki as discussion platform. As these pages are visible for all GerBI participants I would suggest to use English as conversation language as some members are not fluent in German.

I'll also pick up Silke's suggestion to compile a list of which training activities you offer at your facility but I would not only restrict that to actual user training but put together a list with all teaching activities you offer from the facility, e.g. also lectures and seminars.

I put my initials in front of my post so it's directly visible who posted in this discussion forum, would you agree that we proceed like this? We could also use our first names instead?

Cheers, Christian

[AS] Hello together, here is how we do a normal user training in my facility so far: First, we meet up to discuss the project to figure out the best suited scope, preparation strategies and protocols, analysis options and so on. Then, we schedule an appointment for a training at the microscope (normally 1 person at a time, but up to three people per session) and create a profil in our online-booking software (php scheduleit, very close to the one that the MPI in Dresden came up with, but free). After the training, the user is clicked free to use the booking for this scope.

The training normally lasts ~1-1.5h, depending on the microscope and the user. During the training, the user is told about the principles of light microscopy (what is fluorescence, Stoke´s shift, dichroic mirror, how a PMT works, binning of cameras, saturation problems/LUT´s with range indicators, signal-to-noise-ratio, cross-talk/bleed-through, how to check for it/controls/sequential scanning, resolution, NA, Nyquist criteria and so on). We create configurations for their requirements. Possible pitfalls are especially pointed out (like saturation, especially if they are aiming for quantitation). After the training, they normally take an additional hour or so to get to know the microscope themselves. Next time they come, we get them started, but then they are on their own. But they can ask for help any time.

Most users come back to get some help with their analysis, but this really depends on the project. We offer analysis computers with dedicated software like Volocity, Imaris, Huygens but a lot of our users are using ImageJ on their own computers.

As for the lectures: I give talks about the principles of microscopy, different microscope types and techniques (for bachelor and phd students, for future teachers) or more specialized talks about common pitfalls e.g. in confocal microscopy. Right now we have set up a new lecture series for the fall/spring about image analysis and different imaging techniques like FCS and FLIM (will be given bei Steffi Weidenkamp-Peters), 2Ph intravital microscopy (given by Hans Fried) and I will give a talk about superresolution microscopy.

I am sure I missed out on a ton of things but this is a start I guess.

Best, Astrid

Silke's start up procedure


Hi, as we already have a Wiki page describing the "start-up" procedure for a new user in the facility, I will just copy it her, as it is also quite nicely structured already. This is now only the new user training to the facility. We also run general courses on light microscopy and Image analysis, which I will add later on.

The following "box" with my facility registration procedure also contains a few links, which won't work on this page... if you want more information about those terms, let me know and I'll add them. One exception is the "New user project questions" ... I will add those as a new page to the GerBi Wiki as well, as I think its a very nice collections of points every user should think about BEFORE starting on their imaging projects (this collection was put together by Daniel White, a former senior microscopist of the MPI-CBG light microscopy facility).

Ok, so here it comes:

First Contact

  • If you are interested in using our facility please contact silke.white(a) and ask for an introduction
  • In your email please describe your imaging project in as much detail as you can. As a guide, you can have a look at the New user project questions. You don't have to answer all the questions, but the more information you give, the easier it will be for the facility staff to help you.

Admin introduction

Estimated time: about 30 minutes

Booking Database

  • General structure of database.
  • Booking budgets, costs.
  • How to book systems and assistance.
  • How do blockings work. When and why might the facility ask users to give up their slot.
  • How to report a problem.

Booking Rules And Responsibilities

  • Delete and Cancel: the 24h rule.
  • The SIFFY procedure: how to offer and take a free slot.
  • At the end of each session, check booking database: last user / not the last user --> what are the responsibilities?
  • Consequences for failing to switch off a system: extended booking + 15/30min assistant time
  • AND: "END OF SESSION" means: data saved, sample removed, objectives cleaned, software closed ... system is free for the next user!!!

General and Laser Safety

  • The facility is an S1 area - no S2 GMOs allowed!
  • Especially: No eating and drinking in LMF, exception: LMF office
  • Laser safety
  • Waste: General (no S1, no glass, no sharpies); S1 (only solid, take liquid back to home lab); Glass (yellow bins at systems are S1 glass waste); Sharpies (for sharpies only, are S1)


  • Sign the user into the IP-user mailing list
  • Explain IFN Wiki!

Theoretical Background (might be possible without system time)

  • Background to general light microscopy and the techniques that will be used with the system, eg. contrasting techniques, fluorescence, beampath, pinhole, detector etc.

On The System

First Introduction

Usually WITHOUT own sample!!!

Estimated time: system dependent, but usually around 2hours

  • Introduction to hardware: how to switch on/off.
  • Introduction to software: how to properly acquire an image, z-stack, time series (it might sometimes not be possible to cover all of that in the 1st intro).
  • Data handling: explain about original file formats and metadata; advantages/disadvantages of storing data on either hard drive or fileserver
  • Data safety: Point out that the LMF holds no responsibility for data whatsoever!

Important: in order to keep the disk free for imaging - data stored on hard drives older than 1 month will be deleted on an irregular basis without warning.

  • Safety regulations: laser safety, S1 safety, correct use of wastebins.
  • How to clean objectives.

Follow Up Introduction

With own sample!!!

Estimated time: strongly project dependent, but 1-2 hours are usually a good estimate

  • Recap contents of first intro
  • Introduce user to things that couldn't be covered in the first session
  • Help user to set up the system for their own imaging experiment.
  • Stay with user until he/she feels save to use the system independently.

Users are strongly encouraged to contact the IP- team about questions / problems / changes in their imaging projects at any time

[CL] Hey Silke, that was quite detailed and should give us together with Astrid's input a good starting point. Training in my facility runs in a similar fashion to what you both describe, so first a meeting with the new user to discuss the project in general and make him/ her familiar with the admin stuff. Then the training session starts with a safety intro and then I usually do the hands-on and theoretical introduction to the microscope in parallel (takes about 1h for a widefield and about 2h for a confocal). And here comes a question: I usually tell people to bring their own sample to the training session. If their sample doesn't work I take my own ones instead. But I don't do 2 training sessions on a regular basis. I wonder how this works in other places, of course it is desirable to train the user as detailed as possible but I guess everyone has to make compromises due to restrictions in man- (or woman-) power.

Cheers, Christian

[SW] Hi Christian,

I completely understand your point with the manpower. And of course it always depends strongly on the complexity of the system.

However, experience for us showed, that doing 2 introductory sessions in this way greatly relieves the work load afterwards (the same is true for running courses on basic microscopy). The idea behind the "NO own sample for the first intro" is that the users concentrate more on the system itself and on the theory you explain without being disturbed by their biology. If they bring their own sample already to the first intro, they are usually (and naturally) so keen on seeing the final image, that the actual system introduction gets shifted to the background. In those cases we than found to have much more spontaneous "uhm, I'm at the system right now and i just forgot how to… could you maybe quickly explain again…" Whereas, if we give them two introductions in the above described way, they really concentrate on the system itself. The second intro is a good recap for them, most of them will have forgotten one part or the other already and are usually grateful for the reminder. Also, in that session there is than lots of time for really fine tuning the systems for their needs, what with the basics already explained before. The users also usually realized by then that they have much more questions about that whole imaging procedure then before, which then also can nicely be addressed in that session.

After 2 introductory sessions I'd say that 90% of all users are then really confident enough to also use more complex systems independently.

It may create a higher work load for the facility staff in the beginning, but its work load that is easy(ier) to schedule, then spontaneously upcoming (basic) questions afterwards.

I would be very interested, however, to learn that users in other facilities are more confident than ours already after the 1st intro. Maybe we also simply worry too much… ;-)

cheers, Silke

P.s.: Btw., when I say "we" in this case i mean both my facility and the facility at the MPI - CBG here in Dresden (under Jan Peychl). There we "developed" those user introduction procedures and I simply took the idea with me when I left.

[CL] Hi, I fully get your point with the - let's say - psychological advantage of 2 training sessions and I'm quite sure it will also work at my place. I also see how this will work in terms of man-power. Now there's just the point of the supervisor: most won't like it if their students etc. have to spend so many hours before they come home with the first image. This might not be such a big problem if you have already a facility behind you but implementing it in a place where up to a certain point training was just given from users to users I would need to justify that. Here comes GerBI into play: if there was a common standard across imaging facilities it would be easy to justify and implement. So here comes my question: what are the experiences from the others (if not yet stated in this forum), how much training do people need, how's interaction with supervisors and how do you do it in your place?

Suggestions for good imaging practice license

[SD] Hi everybody. Here are my 2 cents on this topic, under a new heading, for better overview. Considering the variability of current instrumentation, I guess there will be no such thing as a one-size-fits-all drivers license. But what we can do is to define specific modules and their (minimal) content, and also modules which are regarded as prerequisite for others. For example such a license could read as:

XY has acquired a GIP license in the following areas:

  • Module Basics of light microscopy (2 h lecture)
  • Module Point scanning confocal microscopy (2 h lecture)
  • Module Live cell microscopy (2 h lecture)

All modules were subject of a written test that XY passed. For content of the modules see the web page of the German BioImaging network. S/he also performed at least 30 hours of confocal microscopy on a (company name) (microscope type).

What we could do as a work group is to define the contents of specific modules. Also, for each module we could define whether listening to the theory is enough, whether a written or oral examination should be part of it and whether practical experience of a certain number of hours should be a requirement for completing the module or whether practical experience could be listed extra.

Some modules I can think of quickly, apart of the ones mentioned:

  • Köhler illumination
  • Phase contrast
  • Fluorescence and fluorescence microscopy
  • spinning disk confocal microscopy
  • 2 Photon excited fluorescence
  • Higher Harmonic Generation microscopy (SHG, THG)
  • How to clean the microscope
  • Digital Imaging (Pixels, Nyquist, ...)
  • CCD and sCMOS Cameras
  • FRAP and its cousins
  • Superresolution basics and modules for the specific techniques.
  • and the list goes on....

As an example for interdependent requirements, a confocal module could require "Basics of light microscopy", "Fluorescence and fluorescence microscopy" and "Digital Imaging" as prerequisite.

Obviously, any kind of standardized training will not cover site specific topics, such as pre-project discussions, length of guided microscopy, data handling, etc. So, in addition to the modules we could establish some recommendations on how to introduce new users, some generalized version of Astrid's and Silke's comments above. Perhaps recommendations would differ for different types of instrumentation.

We could also define some modules for specific, widespread equipments (e.g. there is only a limited number of point scanners out there) but I am not sure this is the way to go.

Concerning the point of man and woman power mentioned above, I agree with Christians last comment. For the purpose of this GerBI discussion I would suggest to ignore of what is possible right now, but instead to focus on what we think is necessary.

Does such a 'modules & recommendations' concept seem to make sense? If so, we could gather a list of modules and everybody could add what s/he thinks should be included. --Steffen 17:27, 14 September 2012 (CEST)

[CL] Hi, I added some stuff to "proposed teaching modules" and structured it a bit. Please feel free to go on editing that section as well as the other sections.

suggestions for the structure of the GIP license

[CL] Ok, I try to refine some stuff, please comment:

  • for the license to get a sort of certificate I think soemone has to meet certain criteria, like e.g. pass a theoretical exam in all of the basic theory and let's say 2 or 3 of the advanced chapters. in addition one should have a record of practical experience in all of the basic stuff and at least 1 or 2 of the advanced techniques. The theoretical part could be covered by a lecture or combination of lecture and seminar. the practical part could be done e.g. in a masters course (maybe combined with the theory) or could be achieved as a trained user in a facility. That also means that the reuirements for the certificate don't have to be achieved just in 1 place or at one occcasion but that people can get it step by setp.
  • for the user training: having a certificate in place would make it easier for e.g. facility staff to see where to start with training, I could imagine that life with new users that already have "the license" might be much easier to deal with

[HF] In general, I like the detailed description of the user training from Silke. We do it in pretty much the same way here in Bonn. One difference might be, that we decide on a case by case basis if we suggest a second training or not. This is due to the enormous background of some of my users in advanced imaging. To be of help to other facilities we should provide (maybe later) some content on the theoretical introductions. As suggested by several of you I also consider individual modules on the different topics (basics in microscopy, fluorescence microscopy, lsm, 2photon microscopy ...) rather effective. Usually a student needs only three or four of these modules as theory background. If it comes to the issue of a GIP license what does it really help? Since I do not know which of the modules the user already got and what in detail has been explained in the modules, I need to go through the whole theory anyway at least briefly. A license will not really help in my point of view, but it will create a lot of additional bureaucratic work. In addition, what if the user is from the states where no such license exists. I think we should pool our efforts and create good basic theory modules. I like the idea to gather the information on workshops and courses you can visit in other facilities and to provide this info on the webpage. Best Hans

[CL] OK, I compiled the stuff that we have at hand for the user training, please look through it and edit it or communicate whether you have any comments/suggestions - thanks.

About Hans' comments:

  • I think the idea with the GIP license is that we come up with something where we can certify a certain level of imaging knowledge. I think we still need to find out what's the best way of doing that. What it should serve for is in my understanding the following:
    • if someone comes to a facility and has the license you can leave off parts of the training which saves you time - however, this might be only marginally for the reasons Hans mentioned
    • the other thing is to get properly trained users/ students something at hand that they can "show off", e.g. if they apply for a job. This in turn will also motivate users/ students to not just sit there if you explain sth but pay attention (as you only get the license if you pass a sort of exam - how can that be realised?)
    • having a curriculum for such a license would also help to ensure a certain standard in bioimaging courses, at the moment we don't even know which courses for basic microscopy skills are around and what is taught there.
  • I think noone wants more bureaucratic work, so if we set something up we should do it in a way that the amount of additional work is minimal. But I guess it will definitely be quite some work to set something like this license up.
  • Having a repository for teaching materials is a good idea. When preparing a lecture or the like I very often spend most of the time searching for e.g. a good schematic drawing and then often end up in creating one by myself - would be great if I could spend that time in another way. What should be in such a repository, in which form and how can we realise that? I guess you don't have something in mind like the Microscopy Primer, as this is already around and a great resource for all of us. In any way we would need to find a place to host such a repository, I can discuss that next week on the meeting.

structuring GIP modules

[CL] OK here a suggestion for restructuring the modules for the GIP:

  1. basic (1 module)
    • basic microscope optics
    • fundamentals of digital imaging
    • how to keep the microscope clean
  2. intermediate modules(require the "basic" module)
    • light sources
    • fluorescence
    • image capturing devices
    • transmitted light modalities I
    • basic image processing
    • How to measure: resolution, chromatic aberration, size (micrometer)
  3. advanced modules (require the "basic" and 1 or more "intermediate" modules)
    • optical sectioning I (requires e.g. "fluorescence" and "image capturing devices")
      1. confocal
      2. deconvolution
    • optical sectioning II (requires "optical sectioning I")
      1. spinning disc
      2. SPIM
      3. etc.

Is having a single "basic" module and the separation between "intermediate" and "advanced" OK? This is just a suggestion (and the list is, of course, by far not complete), please let me know what you think.

[SD]: Christian, I saw your latest comment only now, after I made a suggestion on the main page. Sorry for not trying to include your suggestion, but feel free to do so yourself if you like the concept of the suggestion. --Steffen (talk) 23:18, 6 March 2013 (CET)

"old" module structure, moved from Page to Discussion 7/3/13

proposed teaching modules, option 1



  • basic microscope optics
    • Refraction at the lens surface and chromatic aberration.
    • The compound microscope: beam path and properties of objectives, oculars and condensers
    • Spherical aberration and coverslip thickness
    • setting up Köhler alignment
    • Diffraction and resolution (Airy, Rayleigh, Sparrow, Abbe)
    • Aperture angle, NA and resolution
  • light sources for microscopy (including safety issues)
    • lamps: halogen, metal halide, LED, etc.
    • lasers
  • Transmitted light modalities
    • brightfield
    • Phase contrast
    • Polarization microscopy
    • DIC
    • Darkfield
    • oblique illumination and Hoffman modulation contrast
  • Fluorescence
    • different flavours of fluorophores
    • spectral properties, Stoke's shift etc.
    • Bleaching and counter measures
    • The fluorescence microscope: Filters and their position
    • Bleed through and how to avoid it
    • fluorescence lifetime (as a characteristic of fluorophores)
  • How to clean the microscope
  • image capturing devices
    • Basics of Digital Imaging
      • Pixels and voxels
      • Nyquist
      • dynamic range/ bitdepth
      • signal-to-noise
    • CCD and sCMOS Cameras
      • spectral sensitivity
      • sources of noise
  • basic image processing
  • How to measure: resolution, chromatic aberration, size (micrometer)


  • setting up Köhler alignment
  • image capturing for brightfield and fluorescence
  • basic image processing

proposed course form

  • length for a "covering it all" basic course: 5 full days, including hands-on sessions
  • basic (manual) widefield microscopy setups should be available for hands-on
  • ideal student:teacher ratio: 2 (when including hands-on sessions)
  • max. student:teacher ratio: 4 (when including hands-on sessions)


  • image capturing devices
    • point scanning with PMTs and the like
    • camera lucida
  • optical sectioning
    • standard confocal
    • spinning disk confocal microscopy
    • light sheet microscopy
    • TIRF
  • non-linear imaging
    • Multi-photon excited fluorescence
    • Higher Harmonic Generation microscopy (SHG, THG)
    • CARS
  • fluorescence lifetime imaging
  • FRET
  • looking at molecular dynamics
    • FRAP and its cousins
    • FCS, FCCS
  • Superresolution basics and modules for the specific techniques
  • High Content Screening
  • transmitted light modalities
    • Varel
    • Rheinberg
    • polarisation
  • live imaging
    • live cells
    • intravital

proposed course form

  • each bigger topic could be a half to one day course, ideally including theory and hands-on
  • ideal student:teacher ratio: 2-3 (when including hands-on sessions)
  • ideal student:teacher ratio: 10-15 (for theory only)

go on with discussion from here