User Policy for Otago Centre for Confocal Microscopy

You can read Microscopy Otago's policy document by scrolling down this page (links to sub-sections are below).

Policy Contents (Draft)

Revised: 16 April 2012

1. Introduction

This document contains the various policies that govern access and usage of the Centre. This document must be read, and clearly understood, before any work can commence in the Centre.
The Otago Centre for Confocal Microscopy (OCCM) houses four electron microscopes and a wide range of preparation equipment. It is located next to the Otago Centre for Electron Microscopy (OCEM). These two centres provide a comprehensive and complimentary advanced microscopy facility.

As a regional resource, the OCCM is accessible to all members of the research community.

The host department for administrative and house-keeping purposes is the Department of Anatomy.

The Centre tries to be as responsive as possible to the needs of investigators. If there is an item of equipment you feel would be useful, a technique you feel we should provide, or some other aspect you feel could be improved, please let a staff member know.

Staff of the Centre

Technical Manager: Andrew McNaughton
Project advice, accounts and project costing.

Department of Anatomy
School of Medical Sciences
Telephone ext: 479 7308, Facsimile: 479 7254

Head of Host Department :Professor Dave Grattan
Department of Anatomy
School of Medical Sciences
phone ext: 7364, fax: 479 7254

2.Access, Training and General Procedures

2.1.General access policy

To comply with the Health and Safety Act 1992 all visitors to the Centre must be introduced to a member of the Centre staff, and the purpose of their visit approved.

Staff and students wishing to use the facilities in the Centre must first contact the Technical Manager and complete a 'Project Registration Form'. This form can be picked up from the Centre or downloaded from the Centre's website at;

The approval to use the facilities and equipment in the Centre without supervision (such as before 8:30 a.m. or after 5.00 p.m, or during the weekend) will only be given once competence has been proven. Prior to this, a new investigator is not permitted to work in the Centre unsupervised.

In some circumstances an approved investigator may wish to train a new investigator themselves. Approval to do this will only be given by the OCCM technical manager, and only after discussion with the appropriate contact person.

To comply with the Health and Safety Act 1992 all visitors to the Centre must be introduced to a member of the Centre staff, and the purpose of their visit approved.

2.1.1.Access: practical classes

The facilities of the Centre are available for undergraduate practical classes, undergraduate group projects and postgraduate student training.

Undergraduate Practical Classes
Time and equipment allocation for undergraduate classes will be made available on a "first come, first served" basis.

An application in writing must be made to the Centre Technical Manager, and approved, before any practical classes can be run in the Centre.

The letter of application must include;

(i)the name of the academic responsible for the practical class.
(ii)the dates and times of the practical class (Note: if the practical class is to run after normal working hours, provision must be made for overtime payment)
(iii) the objectives of the practical class, the general content of the practical class and an outline of how the practical class will run.
(iv) the support required from the Centre. This must include specific technical support, equipment that will be used and locations of the practical class.
(v) what handout material will be required to be prepared by the Centre.

Before submitting your application it is advisable to meet with the Technical Manager to discuss the above.

It is important to notify the Centre of your intentions as far in advance as possible. This is to ensure your practical time does not clash with another group and to allow time for any preparation of material.

In all normal circumstances the academic-in-charge of a course or paper must be present during the teaching of that course. Any other arrangement must be agreed to by the Centre Technical Manager.

Before a practical class can commence an account code must be provided to which all the costs incurred will be charged.

2.1.2. Access: postgraduate students

Postgraduate students wishing to use the facilities in the Centre must first discuss their project needs with the Technical Manager of the Centre, and complete a 'Project Registration Form'.

In the case of student investigators, is assumed that the academic merits of the project have been discussed with their supervisor(s), and permission given to undertake the work.

When the project has been approved an OCCM contact person will be assigned. This person will be responsible for all training and supervision of the postgraduate student while in the Centre.

Approval to use the facilities and equipment in the Centre without supervision and/or after hours will be given once competence has been proven in a specific area or task.

2.2. Training

The designated contact person will provide training in all the required electron microscopy preparation techniques, microscope operation and safety procedures required for the successful completion of your project.

No other person is permitted to train a new investigator without the approval of the Technical Manager. This stipulation is to prevent damage to equipment, the dilution of knowledge and to maximise the productivity of the Centre.

The aim of the OCCM training is to enable investigators to obtain the skills to facilitate their ability to work as independently as they desire. Ongoing support and assistance is always available those who wish to achieve a higher level of competence or understanding of the techniques used.

Approval for access may be withdrawn in the event of
investigators neglecting or damaging equipment, using equipment in an
inappropriate manner or in a way for which they have not received
training, neglect of safety and disposal procedures, or admitting
unauthorised persons access to the Centre.

If an investigator has not used an item of equipment for a period exceeding three months they are strongly advised no to use that equipment again until they have had a refresher session.

A high degree of professionalism is expected with regard to equipment usage. Being a multi-user facility any equipment damage due to negligent or inappropriate use may result in other investigators research being compromised. In the case of equipment malfunction please contact one of the Centre technical staff. Users are not permitted to dismantle or attempt to repair the Centre's equipment themselves.

2.3. Level of support

The main functions of the Centre's staff are to maintain
the Centre facilities, train new investigators, develop new
techniques and support undergraduate practical classes. Centre staff
cannot act exclusively as research support staff for individual

It is assumed that prior to the submission of a proposed project the investigator will have completed a literature search to locate methodology papers for their particular specimen. The investigator should have a clear idea of the type of information they require and express this on the Project Registration form.

It is important that the investigator and the contact person (or the OCCM technical manger) understand the aims and scope of the project before commencing work. The onus is on the investigator to ensure that this protocol is appropriate to their specimens, and will provide the answers they seek. In the case where no protocol is provided by the investigator, a protocol can be devised by the Centre staff. This may delay the commencement of the project and no responsibility can be taken for results that differ to that which the investigator envisaged.

The Centre staff are experts in the electron microscopy techniques provided by the Centre. They can offer advice on the suitability of microscopy methods, and on the technical quality of the microscopy data. It is not their job to interpret findings, since they are unlikely to be specialists in the investigator's particular field. Interpretation and analysis of images obtained from the microscopes is ultimately the responsibility of the investigator, or, in the case of students, their academic supervisor(s).

2.4. Work priority

Priorities are set by the Technical Manager in consultation with Centre staff and users. Teaching commitments (undergraduate and postgraduate) generally take precedence over other work.

As a regional resource, the Otago Centre for Confocal Microscopy is accessible to all members of the University research and teaching community. Researchers from departments that provide support under the club funding model are given priority during times of heavy usage.

2.5. Liability

Work is undertaken in the Centre on the understanding that it will be done to the best of the Centre staffs' ability, and in good faith. However, the nature of electron microscopy is such that the various techniques do not always produce consistent or expected results. It is assumed the investigator understands this.

Where equipment not belonging to the Centre is brought into the Centre's laboratories, this equipment must comply with New Zealand safety regulations; electrical equipment must show a current electrical safety test label to indicate compliance with AS/NZS 3760. The use of any such equipment is at the discretion of the Centre's staff and liability for damage that occurs to the equipment while in the Centre resides with the owner.

The Centre will not be liable for any delay, non-performance or loss of specimen arising from or attributable to circumstances beyond its direct control. Delays may result from, but are not limited to, inadequate instruction, equipment malfunction, delays in the supply of goods and services to the Centre and labour disputes.

The Centre will use its best endeavours to achieve the projects aims at the estimated cost and shall apply all resources which are necessary to achieve the project aims.

Any exceptions to the above apply only when the level of liability of the Centre has been agreed to by both parties after negotiation. The agreement must be in writing and signed by both parties prior to the start of the project.

2.6. Reserving equipment

2.7.1. Making bookings

Most major items of equipment in the OCCM must be booked prior to use. Bookings should be made via the web-based system ('Calcium' software) once access to the system is made available to the investigator. The booking system is for equipment only and new investigators will usually require the supervision of an OCCM staff member when using the equipment. Therefore, unless specifically told otherwise, new investigators should not book equipment without checking with their contact person first.

Bookings can be made for a maximum of two weeks in advance, that is, the current week plus the week following (booking for undergraduate practical classes and maintenance/repair work are exceptions).

2.7.2. Cancellation policy

All book-able equipment and the imaging facilities have a "turn up" time of 15 minutes after the booked time has started. If you are running late you are requested to phone and indicate that you will be late, but that you still want your booked time. A note to this effect will be placed on the appropriate equipment

If you do not arrive in the "turn up" time, and do not ring to indicate you still want your booked time, the booked time may be used by another investigator.

At times of high usage the number of time slots available to any one investigator on the electron microscopes are subject to the following rules;

(i) no more than four consecutive slots may be booked on any one day.

(ii) no investigator may book more than six slots between the hours of 8.30 a.m and 5.00 p.m, in any one week. Extra time is available in the evenings and weekends for approved operators only.

2.8. Supervision and after-hours access

Initially, a new investigator is not allowed to work in the Centre without supervision, and is not allowed to work in the Centre after hours.

Approval to use the facilities and equipment in the Centre without supervision and/or after hours will be given by the appointed contact person or the technical manager, once competence has been proven.

It is the responsibility of all investigators to ensure that the equipment they use is left ready for the next investigator at the end of their session. In particular, rooms and equipment must be left clean, tidy and operational for the next user. If you have been using one of the microscopes please ensure you have followed the instructions on the notice "Before You Leave the Microscope Room". This notice can be found by the door, and also gives the phone numbers of the Centre staff to contact in case of problems.

In the case of equipment malfunction after hours, users should attempt to contact one of the Centre staff. A list of home phone numbers is on the wall near the light switch. However if this is not successful then the equipment should be turned off, and a note left explaining the nature of the malfunction, the user's name and contact phone number for the following day. An 'Out of Order' tag should be applied to faulty electrical equipment. These tags can be found on the noticeboard in B14.

In the case of damage caused by negligent use or unapproved use the cost of the repair will be charged to the individual who caused the damage. Accidental damage will be paid for by the Centre.


2.9.1. Keys

Keys are available to approved investigators for access to the Centre, and for other locked resources as required. When the project is completed, all keys issued must be returned to the Centre.
Keys must never be passed to a third party. The Centre must be notified immediately if a key is lost.

2.9.2.Security after hours

When leaving the Centre during the day, and if no staff are around, you are required to lock the door that you leave by. This applies even if you are leaving for only a short period.

If you are the last person to leave the Centre at the end of the day please ensure;

-all the lights in the area you were working in are turned off
-any gas outlets you may have used are off
-all taps are turned off, especially important in the preparation lab
-the door is locked behind you.

Please report any suspicious behaviour in the basement area at any time to a Centre staff member, or the University Security Centre, phone 5000 .

2.9.3.Desk Areas

A staff member's desk area and computer is that staff member's personal space. These areas may contain items and information confidential to the staff member. It is expected that users of the OCCM will respect the personal nature of the staff desk areas. OCM staff computers are not available to OCCM users without explicit permission form the staff member concerned or the Technical Manager.

2.10.Library and image resources

The Centre maintains a comprehensive book library, literature reprints and a digital image and 35mm slide collection. All are available for use by Centre users.

Removing books from the Centre is not encouraged. However, if this is required, a book loan form must be filled in and given to one of the Centre staff. A return date will be required.
If the book is not returned within a reasonable period after the return date the borrower may be charged the replacement cost of the book.



The Otago Centre for Confocal Microscopy (OCCM) is committed to the protection of its staff, users and visitors. Safety will take precedence over all other activities at all times.

In meeting this commitment, the OCCM will;

1.Do everything possible to ensure a safe workplace and safe equipment.
2.Establish and insist upon safe methods and safe practices at all times.
3.Comply with all legislative requirements.
4.Ensure all persons understand and accept their responsibility to promote a safe workplace.

Likewise users of the facilities in the Centre have a responsibility to observe safe work practices relating to their work in the Centre.
Responsibilities of OCCM Users:
-take responsibility for their own health and safety while working in the Centre.
-to know and follow all OCCM Health and Safety procedures and participate in improving procedures.

The appointed contact person will introduce new investigators to the current Centre safety procedures and disposal methods. Failure to abide by these procedures will result in access to the Centre being withdrawn.


Lab coats that adequately cover the body must be worn at all times in the preparation laboratory. For the laboratory designated 'PC Clinical' (B14) suitable lab coats will be provided for use only in that room.

The wearing of jandals or other open-top footwear is not permitted in the specimen preparation areas and in any area where liquid nitrogen is being used.

3.3.Eating and drinking

Eating and drinking should be confined to B17 or the Departmental tearoom (third floor) wherever possible. Eating and drinking in the preparation areas and the microscope rooms is not permitted under any circumstances.


All accidents and spillages of dangerous materials must be reported to a member of the OCCM staff as soon as possible. It is University of Otago policy that such accidents and incidents are reported on a University of Otago Accident/Incident Report Form. The forms are available in the Centre.

3.5.Infectious agents/hazardous chemicals

Investigators intending to bring infectious agents and/or hazardous chemicals to the Centre must first submit a Letter of Intent' to the OCCM Technical Manager outlining their purpose, the risk involved, the precautions that will be taken to reduce the risk, the spillage mop up procedures and the disposal procedures that will apply.

For hazardous chemicals that are unknown to the Centre staff a Material Safety Data Sheet (MSDS) must be provided with the 'Letter of Intent'.

The Letter of Intent' must be approved by the Departmental Health and Safety Adviser and the OCCM Technical Manager before the infectious agents and/or toxic chemicals can be brought into the Centre.

No specimens suspected of containing the causative agent of Creutzfeldt-Jakob Disease or other human transmissible Spongiform Encephalopathies are permitted in the Centre. No specimens containing high risk infectious agents are permitted in the Centre.

All spillages involving human tissue must be cleaned up quickly using the appropriate clean up method, and the OCCM Technical Manager notified.

Any specimens requiring PC2 level containment conditions must have this requirement noted on the Project Registration Form.

3.6.Specimen preparation laboratory (PC2 Clinical)

The specimen preparation lab is designated PC2 Clinical under MAF Regulation Standards for Containment Facilities and Transitional Facilities. Because of the multi-user nature of the laboratory and the type of specimens and chemicals present in this laboratory it is critical that users adhere to the PC2 Clinical guidelines.

It is the responsibility of all who use this laboratory to tidy up their work area immediately after they have finished. Cleaning up includes;

- cleaning all glassware used and placing it on the draining rack to dry
- safely and correctly disposing of all biohazards, chemical waste and physical waste
- recording all costs incurred
- reporting any shortages of chemicals and materials

3.7. Equipment faults

In the case of equipment malfunction please contact one of the Centre technical staff. Users are not permitted to dismantle or attempt to repair the Centre's equipment. An 'Out of Order' tag should be applied to faulty electrical equipment. These tags can be found on the noticeboard in B14.

4.Charging Policy

The Otago Centre for Electron Microscopy operates a cost recovery budget. Before work can commence in the Centre an account code must be supplied to which the costs incurred can be charged.

Before work can commence agreement must be reached as to whether the project is subject to full cost recovery charges or internal cost recovery charges. If the source of the funding is from a full cost recovery funding organisation, or a source external to the University, full cost recovery charges will normally apply.

For those who undertake their own work in the the Centre, an honesty system of cost recovery operates. Each user is required to record their own expenditure on the appropriate cost recording system (either paper based or the computer terminals).

Failure to comply with this system will result in access to the Centre being withdrawn.

Project costings can be provided if required. At least two weeks notice must be given if this service is required. Information about the cost of a project as it proceeds can also be provided. Arrangement for this service must be made with the Technical Manger.

Current charge rates can be found in appendix 2.

The OCCM (or its administrative committees) reserves the right to reconsider the Charging Policy at any time.

5.Specimen and Data Ownership

Specimens provided by investigators remain the property of the investigator unless it is made explicitly clear otherwise. Specimens can be stored in the Centre. This is at the owners' risk.

Electron microscope data (images and analysis information), either in digital form, hard copy or negatives, are the property of the investigator. However, on request, they can be stored in the Centre. This is at the owners' risk.

6.Acknowledgement of the Centre

One of the measures of the Centre's effectiveness is the record of published and/or presented results obtained from work carried out in the Centre. It is important that the Centre has an up-to-date list of publications resulting from the work done here. This information is used vital to support applications for equipment grants and important for the long term security of the Centre, .

Published work includes oral and poster presentations at seminars and conferences as well as theses and papers. As the Centre is a facility which investigators tend to use and then move on, an acknowledgment can be overlooked by the time the work is published. If the resources of the Centre contributed in any way to a publication, there should be a general acknowledgement to the Otago Centre for Confocal Microscopy. Where individual Centre staff have contributed the bulk of the technical microscopy work, a specific acknowledgement is expected.

Co-authorship should be considered where an OCCM staff member has made a significant intellectual contribution (such as developing specific techniques for the project) and/or has been significantly involved in writing the manuscript. It is expected any acknowledgements be made with the full awareness of the Centre staff member concerned and that they have been provided with a copy of the final work, where this is feasible. It is expected that they be provided with sufficient information for them to judge the appropriateness of the microscopy data in the context of the published work.

This information be forwarded to the EM Centre Technical Manger. A list of the equipment suppliers can be found on the Centre's website. For help in acknowledging the facility, please refer to your contact person or the Technical Manger.

7.Complaints Policy

Complaints of any nature regarding the Centre and its staff should be directed to the Technical Manager.

If, after discussion with the Technical Manager, a satisfactory resolution is not found then the matter will go directly to the Head of Department (HOD), Department of Anatomy and Structural Biology.

Appendix 1

Specific potential hazard list

- all biological material, whether it is animal, human, plant or microbiological must be treated as potentially infectious (by inhalation or contact).

- all the chemicals used should be treated as potentially toxic unless known otherwise, ie carcinogens, mutagens or poisons. Exposure to most of the chemicals is potentially lethal.
-be aware of exposure limits and TLV values. All chemicals have these values.
- chemicals may cause explosions - contact explosions e.g. Picric Acid, or compatibility explosions e.g. epoxy resin and acrylic resin..
- chemicals may not be compatible and may react, e.g. nitric acid and ethanol.
- chemicals must be disposed of correctly.

Liquid Gases; (liquid nitrogen, propane, liquid CO2)
- contact with cryogenic liquid gases can result in cryoburns: wear protective gloves and face mask. Your eyes are especially vulnerable.
- asphyxiation: use these gases in a well ventilated room
- ignition explosion: avoid ignition sources and use in well ventilated room
- pressure explosion: use only a purpose-deigned, vented dewar when transporting liquid gases.

Electrical: shock, fire, explosion

Mechanical; burns, cuts, pressure vessel breakage

Processing samples for transmission electron microscopy includes many potentially hazardous situations. The dangers include:
- collecting specimens; biohazards, cuts.
- primary fixation; all fixatives are toxic, some buffers are also toxic.
- secondary fixation; all fixatives are toxic, some buffers are toxic.
- dehydration; all solvents are toxic, incompatibility of chemicals, fire hazard.
- infiltration; propylene oxide is carcinogenic.
- embedding; resins are carcinogenic and mutagenic.
- sectioning; cuts, semi-thin section stains are toxic.
- staining; heavy metal poisoning.

Processing samples for scanning electron microscopy include many potentially hazardous situations. The dangers include:
- collecting specimens; biohazard, cuts.
- fixation; all fixatives are toxic, some buffers are toxic.
- dehydration; all solvents are toxic, incompatibility of chemicals, fire
- critical point drying; explosion, asphyxiation.
- sputter coating; explosion.
- liquid gases - see comments above

Appendix 2

Labour Charges

$35 per hour: Staff and students from all University of Otago departments except the club funding participating departments (unless the project is funded from a full cost funded research grant).

$50 per hour: External clients and staff or students on full cost funded research grants.

No charge: Staff and students from the club funding participating departments (except for staff on identifiable full cost funded research grants).


1) Protocol development.
2) Initial training of new users and advanced training of existing users.
3) Undergraduate practical sessions for all University of Otago departments except club funding participating departments.


1) Initial consultation about a new project, either internal or external investigator.
2) The first 30 minutes of each consultation with regard to technical advice or problem solving.
3) Equipment maintenance and repair time.
4) Centre housekeeping and health and safety duties.
5) Professional development time of Centre staff.
6) Development of new techniques.
7) General problem solving activities.
8) Community and promotional activities.

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