Prior to having an account with the Microscopy, users are required to attend a Microscopy Fundamentals Training Course. This course provides a general introduction to the principles and applications of microscopy, including optics, microscope design, transmitted light techniques, fluorescence and confocal microscopy. The cost for the course is $50 per person, and this will be deducted from the first hour of microscope use. To register for the course, please send an email with contact information and a grant number to tdiefenbach@partners.org. Occasionally, more advanced training courses will be offered and, although not a requirement, current Microscopy users are encouraged to attend.

Individual Training
Individual training is provided on the Zeiss LSM 510 confocal microscope, the Zeiss Axio Observer Automated fluorescence microscope, the Zeiss MIRAX MIDI slide scanner, and the Zeiss Axio Observer A1 manual microscope. Training on the LSM 510 is a 2 hr session, training on the Zeiss Axio Observer Automated microscope is a 2.5 hr session, training on the Zeiss MIRAX MIDI is 1 hr, and training on the Zeiss Axio Observer A1 system is 1 hour. Each training session costs $60/hr. Samples suited to the training session are supplied so users do not bring their own samples to the training sessions. Training covers the microscope and associated hardware in addition to in-depth orientation on the “Zen” confocal software from Zeiss as well as the Metamorph imaging software for the automated Axio Observer. At this time, users will be given individual computer login IDs where applicable in addition to a password provided by Microscopy. Refresher training courses are available upon request. All users are to be trained only by qualified Microscopy staff. Training of new users by previous users is not permitted.

Training and consultation in image analysis for either the Metamorph or Imaris is presently provided at no charge.

Equipment Locations
The Zeiss LSM 510 confocal microscope is located on the 5th floor of CNY 149 in the Charlestown Navy Yard, Room 5.214E in the Infectious Disease Unit. This is also the location for the Zeiss Axio Observer Z1/RPI automated fluorescence microscope. These two systems are housed in BL2+ faclities, and therefore users are required to adhere to BL2+ regulations when using either microscope system.

The Zeiss MIRAX MIDI slide scanner is located in Room 5.214K.

The Zeiss Axio Observer A1 manual microscope is located in Room 5.553. A second image analysis workstation with Imaris software is located on the 6th floor of CNY 149, Room 6.613. Presently there is no charge for use of image analysis workstations, however the training charge for image analysis is the same hourly rate as for the imaging instruments.

Reserving Time on the Equipment
Once users have received the appropriate training, time may be reserved online for the different microscope systems available. Time on the equipment must be booked in advance.

For unassisted (independent) users, online booking of the Zeiss LSM 510 confocal microscope the Zeiss/RPI Axio Observer automated fluorescence imaging system, the Zeiss MIRAX MIDI slide scanner, and the Zeiss Axio Observer A1 manual microscope can be made here:

www.schedulebook.com

Only users who have been trained on these instruments will be given schedulebook access to them. Prior to booking time on the microscopes, users are required to complete the course and individual training components and will then be provided with a user ID and password for the online booking system. If they miss the microscopy training course, users may sign up for the next scheduled course to fulfill their requirements. All Microscopy users are required to schedule their time through the online Schedulebook account ahead of their intended usage time to avoid scheduling conflicts. For the Axio Observer A1 microscope, users may only require a few minutes to check their samples. In this case prior scheduling is not required, however users then must vacate the microscope for someone who has scheduled time online, whether to use the microscope or the Metamorph image analysis workstation. For all other instruments in Microscopy, prior reservation using Schedulebook is required. Even if the user makes a last minute decision to go on an instrument that appears unoccupied, they are required to show they will be occupying the instrument through Schedulebook as a courtesy to other users. If users are unable to make their scheduled time, please leave a note on Schedulebook about that so that other users are aware the system will be occupied, otherwise please remove your scheduled time immediately so that other users may see that it is free and take up that timeslot. If users are more than 30 minutes late for their scheduled time, and leave no notification on Schedulebook indicating they still plan to use the system, they then forfeit their scheduled time and another user may go on the system.

It is important that any and all use of Microscopy equipment must be logged on the user log sheets provided next to each imaging system. Users filling out log sheets should print clearly and remember to provide both the start and end times for their session. As long as imaging equipment is left on, and the time is reserved on Schedulebook, that time will be billable. Users failing to report their time on the log sheet will be billed according to their Schedulebook time, but in all other instances, the log sheet will be referred to for billing purposes.

Assisted Imaging
For those requiring assistance with their imaging, bookings are made by contacting tdiefenbach@partners.org to schedule an imaging session. Assisted imaging can consist in the guidance of the user in the proper techniques and approaches during their imaging session (directed service). It can also consist in the user providing samples ready for imaging, and being present for the duration of the imaging session to provide guidance as to the images to be obtained (full service). For either service, users are fully responsible for their samples and data management and are charged the assisted rate.

Microscope Use Policy
For any of the imaging systems used in the core, users are required to fill out the imaging log sheet found next to each imaging system and include the date, their name, their PI's name, the time they turned on or began using the system and the time they finished with the system. Users are also required to make a record on the imaging log sheet whether there were any technical issues during imaging.

In order to balance the amount of user time for each piece of equipment, a maximum use policy will be in effect on a per week basis. Each individual user may book up to two 3-hour sessions per week on the confocal microscope during regular hours (9:00am-5:00pm Mon-Fri), with unlimited time after hours and on weekends. Users are encouraged to schedule as far ahead of time for their imaging sessions as possible.

The exception to the session quota is if on the actual day of scheduling there is free time during working hours still remaining on the confocal microscope. If by 10:00am the morning of that same day there is still time available, users who are at their time quota for the week may book and use any free time on or after 10:00am. Users with quota time remaining should therefore book for same-day imaging that morning before 10:00am, otherwise free time remaining will be open to all users regardless of their quota. Again, this exception only applies for bookings made on the day of imaging. For projects requiring additional time per week, special arrangements may be made with Microscopy management.

If you need to cancel your scheduled booking, please do so a minimum of 24 hours prior to the booked time so that others may utilize the canceled time-slot. Users may be charged for time scheduled if they do not consistently cancel their booking on the online calendar in a timely fashion. If users are more than 30 minutes late for their scheduled time-slot, they may lose their time-slot to the next user, unless they indicate that they will be delayed through a note in Schedulebook for that reserved time. Users who do not use their scheduled time and do not remove their scheduled time from the online calendars, or notify Microscopy that they are unable to use that time, will be charged at the unassisted use rate for the time they scheduled. Again, users should ensure they print clearly on the log sheets.

Microscope users are responsible for maintaining a clean working area around the microscope. Objects are not to be placed on the vibration isolation tables, nor may users lean on the tables apart from the provided arm supports. Users are responsible for reporting any problems with the imaging equipment or software, preferably as soon as possible after the problem occurs. In using the equipment, users agree to immediately report any instrument malfunction or damage to the Microscopy staff. If ever in doubt on how to use a piece of equipment, users should ask the Core staff rather than attempting to operate or set up the instrument themselves.

There are three kinds of objectives on Microscopy microscopes, air, oil and water immersion objectives. Most often users will be using the air or oil immersion objectives. Care should be exercised in making sure that only a minimum amount of oil is used on the oil objectives (typically one small drop of oil on the objective per glass slide) and that when switching back to a lower power air objective, oil is not transferred from the glass slide to the air objective. Excess oil should be wiped off the objective using only the lens tissue paper provided (use two or more sheets of tissue folded twice). Under no circumstances may users clean objective lenses with solvents of any kind. If objectives appear dirty, users may request Microscopy staff to clean them. Also under no circumstances may users borrow or transfer objective lenses to other microscopes.

Users who know from the schedule that they are the last of the day are required to perform the shutdown procedure for the equipment.

For imaging instruments that have a mercury arc lamp or XCite arc lamp light source, if a user knows that someone will be using the equipment after them within two hours from when they are finished, they should leave the arc lamp on for the reason that turning on and off the lamp significantly reduces the lifetime of the bulb. If they are not sure that someone will be coming later on to use the microscope, they can check Schedulebook. If it is the end of the day, and they turn off the arc lamp, they should make a note of the time it was turned off in case someone comes within 15 min later to turn it on again, so that the arc lamp is not turned on when hot.

Users of the Axio Observer A1 microscope who are simply checking their samples for fluorescence must leave the XCite arc lamp on for at least 45 min once it has been turned on, regardless of how long they take to look at their cells. Once turned off, the XCite arc lamps must be left off for 15 min prior to turning on again in order to cool down the bulb to avoid premature wear of the bulb and reducing the chance of the bulb exploding. Users will only be charged for their use time in that instance, but must indicate when they turned on and off the arc lamp, so the next user will know whether to wait or not before turning it on again.

Users are prohibited from modifying or in any way attempting to repair or troubleshoot any piece of Microscopy equipment if there is a hardware or software problem (apart from restarting the software or hardware as trained). In the event of a problem that affects the operation of the equipment, please contact Microscopy staff.

Data Management
All users are responsible for the saving, storage or backup of any data obtained using Microscopy equipment. Therefore, users are required to back up their data after each imaging session, and should allocate the appropriate amount of time (5-10 min) at the end of each imaging session for that purpose. Data may be backed up on Microscopy computers through user-supplied CDs, DVDs, USB flash drives or USB external hard drives. Since digital imaging often requires GB worth of data, users should be prepared to manage large amounts of image data, as the imaging computers have limited hard drive space. In the event that users run out of time and cannot back up their data at the end of their session, they should set up time at the end of the day to make sure it is properly backed up. Users are not permitted to disturb other subsequent users in order to obtain their data from the computer, and must wait until there is free time on the instrument to back up their data. It is advisable for users to wait until they have the data transferred to another computer and confirm that the data is free of corruption prior to deleting it from the Microscopy computers in order to avoid lost data, again as Microscopy is not responsible for lost or corrupt data. Periodically, the data drives on the imaging computers will be cleared so users must ensure timely backup of their data. For users using USB flash drives to transfer data, every effort should be made to confirm that their drives are free of computer viruses or the like prior to using it on Microscopy computers.

Note: Microscopy policies are subject to change so if in doubt about a particular policy please contact Microscopy staff.