Use of Olympus IX81 Microscope for Fluorescence Imaging with a

Use of Olympus IX81 Microscope for Fluorescence Imaging with a

Microscopy and Imaging Center, Texas A & M University http://microscopy.tamu.edu

–Fluorescence Imaging with Olympus IX81 Microscope

1

Last updated August 27, 2013

Contents

Mercury Lamp Precautions ................................................................................................................................................1

Acknowledgment policies ..................................................................................................................................................2

Description of the microscope for your “Materials and Methods” ....................................................................................2

Biosafety requirements and rules for work in the MIC ......................................................................................................2

Biological Spill Response: BL1 Laborator y .......................................................................................................................4

STARTUP PROCEDURE .................................................................................................................................................5

Using the Olympus IX81 microscope ................................................................................................................................6

Adjusting the oculars for optimal viewing ....................................................................................................................6

Focusing ........................................................................................................................................................................6

Seting up Köhler illumination .......................................................................................................................................7

Differential Interference Contrast (DIC, a.k.a. Nomarski) observations .......................................................................8

Using the 20x and 40x dry objectives- how to keep them clean: ..................................................................................9

Using and cleaning the oil immersion objectives: .........................................................................................................9

Using the 60x/1.2 Water Immersion objective ............................................................................................................ 10

CLEANING ................................................................................................................................................................ 10

Using objectives with coverslip thickness correction ................................................................................................. 10

Fluorescence microscopy ............................................................................................................................................ 11

CCD camera imaging ....................................................................................................................................................... 12

Multidimensional Acquisition ..................................................................................................................................... 13

XY Pixel size, Recommended Z-step, Sampling and Nyquist Criterion ......................................................................... 14

Data management and conversion ................................................................................................................................... 15

Storing your data ......................................................................................................................................................... 15

Viewing and processing the image files ...................................................................................................................... 15

Data Conversion .......................................................................................................................................................... 15

SHUTDOWN PROCEDURE .......................................................................................................................................... 17

Laser turn off procedure: ................................................................................................................................................. 17

Each new user must be trained by the MIC staff. Second-hand learning from another user is not sufficient to gain user status.

Even though no lasers are used for wide-field fluorescence imaging, the microscope is a part of the laser scanning confocal system and all users MUST take the online Laser Safety course, located at https://ehsdtraining.tamu.edu

, before their first training session.

Standard operating procedure (SOP) and a copy of Texas Administrative Code §289.301

(Registration and Radiation Safety Requirements for Lasers) are located in the confocal microscope room.

The last user must be able to properly shut down the entire system, including the lasers if they were left on by the previous user.

Mercury Lamp Precautions

• The lamp emits strong UV and visible radiation. Do not look into the source or disassemble the lamp housing.

Do not turn the lamp on if the lamp usage counter reached its expected lifetime (300hr)!

• After turned on, it takes ~ 15 min for the lamp to reach full brightness.

• Lamp must be ON for at least 30 min before it can be switched OFF.

• After the lamp has been switched OFF, it must cool down (~15 min) before it may be switched

ON again.

Microscopy and Imaging Center, Texas A & M University http://microscopy.tamu.edu

Acknowledgment policies

2

MIC guidelines mandate that the use of the microscope must be properly acknowledged in any publication (including web pages). You can use the following statement:

“The use of the Microscopy and Imaging Center facility at Texas A&M University is

acknowledged.

Users are also required to file a copy of any relevant publication containing the acknowledgment with the MCF administrative office.

Description of the microscope for your

“Materials and Methods”

Here is an example; please modify the filter selection and objectives used as needed:

Microscopy was performed using Olympus IX-81 inverted microscope (Olympus America, Center Valley PA, USA) equipped with UPLSAPO 100x/1.4 oil immersion objective, a Rolera XR CCD camera (Qimaging, Surrey BC, Canada) and a Proscan H117 motorized XY stage (Prior Scientific, Rockland, MA, USA) controlled by the µManager freeware

(http://www.micro-manager.org). A field lens of 1.6x magnification was used to achieve Nyquist sampling for imaging with the 100x objective. The following fluorescence filter sets (Chroma Technology Corp., Bellows Falls, VT, USA) were used, with the central wavelength and bandwidth of the excitation and emission filters as indicated:

HQ-Cy3 (Excitation 545/30 nm; Emission 610/75 nm); YFP (Ex. 500/20; Em. 535/30); GFP ( Ex. 470/40; Em. 525/50);

CFP (Ex. 436/20; Em. 480/40); DAPI (Ex. 350/50; Em. 460/50); Texas Red (Ex. 560/55; Em. 645/75).

Biosafety requirements and rules for work in the MIC

Selected rooms in the Microscopy and Imaging Center (MIC) have been approved as BL-1 space.

In order to be able to bring the active BL-1 material to the MIC, the MIC facility and room number

MUST be listed in the investigator’s IBC permit, in Section F, Agent use and Storage Locations. The investigator is required to send a copy of the IBC permit listing the relevant MIC lab and the BL1 organisms, to MIC office ( [email protected]

), BEFORE bringing the BL-1 samples.

The MIC is neither equipped nor allowed to deal with samples that are Biosafety level 2 (BL-2) or higher. If such samples need to be examined in the MIC, they must be rendered inactive prior to their transport to MIC. The investigator should first contact the University Biosafety Committee (IBC) and have an approved operation procedure for sample inactivation and containment. The investigator should consult with MIC to make sure that the procedure is compatible with microscopy imaging.

F. Agent use and storage locations.

Location

ID

1

Campus

Texas A&M

Building

Number

1530

2

3

4

Texas A&M 1530

Texas A&M 1530

Texas A&M 1530

Room

Number

1116

1117

1118

1121

Room

Use

Multiphoton microscopy

Cell and tissue culture

Confocal microscopy laboratory

Current

Bio-safety Level

BSL-1

BSL-1

BSL-1

BSL-1

Shared

Lab?

Yes

Yes

Yes

Yes

Other

PIs

*

*

*

*

5

Texas A&M 1530 1120

Micropscopy room

BSL-1 Yes *

* The list of other PIs is maintained by the MIC

All users of rooms listed in table F must follow the rules. This applies even to those users that do not work with samples requiring IBC permit:

Microscopy and Imaging Center, Texas A & M University http://microscopy.tamu.edu

I) For users that DO NOT work with BL-1 agents:

- Closed toe shoes are required in the confocal microscope room. Upon exiting the microscope room, users are required to wash hands. The sink in the Bioprep lab (Rm. 1121) or in the Culture

3 room (Rm. 1117) may be used.

II) For users working with active BL1-agents:

- The MIC facility and room number MUST be listed in the investigator's IBC permit, in Section F,

Agent use and Storage Locations; The PI is required to send a copy of the IBC permit, listing the relevant MIC lab and the BL-1 organisms, to [email protected]

BEFORE the BL-1 samples can be brought to the MIC. Without the MIC facility listed in the PI’s permit, no BL-1 work is allowed in the MIC.

- Samples being brought to the MIC must be contained, in accordance with the operating procedure in investigator’s IBC permit, to prevent spills during transport

- Closed toe shoes must be worn

- The use of gloves should be restricted to only handling the sample to avoid contaminating general work area. Touching the microscope or the control computer keyboard and mouse with gloved hands should be avoided. Gloves may not be worn outside of the rooms listed in table F.

- The user must ensure proper disposal of the samples - taking all samples as well as contaminated microscope slides, etc..., back to his/her laboratory for disposal. Samples may not be put in regular trash in the MIC.

- Any spills and contaminations must be cleaned up, decontaminated by the user and the emergency contact person notified.

- At the end of the work session, the work area, including the microscope stage must be wiped clean using a disinfectant (70% ethanol or disinfecting wipes). Detailed instructions will be given by MIC staff as needed to ensure proper disinfection, while preventing damage to the instrument.

- Upon exiting the BL-1 work area, users must wash hands. The sink in the Bioprep lab (Rm. 1121) or in the Culture room (Rm. 1117) may be used.

Microscopy and Imaging Center, Texas A & M University http://microscopy.tamu.edu

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Biological Spill Response: BL1 Laborator y

The following procedures are provided as a guideline for biohazard spill clean up in a BL1 laboratory. Although the biological material in a BL1 level spill should not be a significant health hazard, you have the obligation to minimize the release of recombinant organisms and biohazardous material from the laboratory.

In the event of a spill:

• If a biohazardous material spills on you, remove any contaminated clothing and wash any exposed body parts.

• If a biohazardous material gets in your eyes, flush at the nearest eyewash station.

• If the spill area is large or in a common use area, mark, label, or otherwise denote the area so others may avoid it.

• Using materials from your spill kit:

– Put on gloves, lab coat, and eye protection.

– Cover the spill with absorbent material.

– Pour disinfectant over the entire area. Allow the area to soak for 30 minutes.

• If warranted, contact the principal investigator, assess the magnitude of the spill, and formulate further plans of action.

• Safely pick up any broken glass with forceps or sweep into a dustpan, and dispose the residue into a broken glass/sharps container.

• Place spill materials into an autoclave bag.

• Make sure area is cleaned and disinfected thoroughly.

• Soak any contaminated clothes and shoes in a tray with disinfectant.

• If the spill is greater than 25 ml or contains recombinant DNA, report the spill to the

Office of Research Compliance and Biosafety at 979.862.4549.

http://rcb.tamu.edu

Microscopy and Imaging Center, Texas A & M University http://microscopy.tamu.edu

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STARTUP PROCEDURE

1. Fill out the log sheet, including the account number and your full name or last name.

2. Turn on the following components (the order is important!):

Mercury Lamp Power Supply. If the time counter exceeds 300 hours, do not turn it on, ask MIC Staff to replace the Hg lamp)

Microscope Control Box,

Prior Optiscan stage controller

Computer

CCD camera

3. Log in the computer: User = Fluoview Password =

4. Open the software: “Micromanager”. When prompted for the name of the configuration file, choose YOUR config file, located in the MicroManager installation directory, e.g.,

"C:/Program Files/Micro-Manager-1.4/MMconfig_Carol_V.cfg"

Figure 1. Loading a configuration file

The software now tries to take control of the microscope and other hardware. If you get error messages, try re-loading the hardware configuration (Tools - Load Hardware Configuration).

You can change/modify the configuration file as needed and save it with a different name.

Microscopy and Imaging Center, Texas A & M University http://microscopy.tamu.edu

Using the Olympus IX81 microscope

Adjusting the oculars for optimal viewing

1. Adjust the interpupillary distance of the binoculars so that you can see with both eyes

2. Set both oculars to “0” focal correction (see scale on the side of the ocular tube)

3. Use the microscope focus knob to bring the specimen in focus for your left eye.

4. Now, take your hand off the focus knob. Turning the ocular focus correction, bring the specimen in focus for your right eye.

Focusing

Turning the microscope focus wheel towards you will move the objectives upwards, closer towards the specimen (= focus into the specimen). Turning the focus knob away from you will lower the objective, i.e., move it away from the specimen.

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Seting up Köhler illumination

The most overlooked component of a modern microscope is the condenser. It is a lens system that focuses the illuminating beam on the specimen and limits the resolving power of most microscopic applications. Kohler illumination produces an even field of illumination by focusing the plane of the field-limiting aperture onto the specimen plane. The optical corrections made in the objectives lenses are designed to work best with Kohler illumination. A few seconds spent properly

adjusting the condenser will greatly improve the resolving power of the microscope and is

absolutely necessary for many of the more sophisticated techniques.

1. Place specimen on the stage, and switch to the DIC filter (in software). Make sure the microscope is set to visual observation, not the camera port (top left button on the front of the microscope).

2. Focus the specimen (Fig. 2A). From now on, do not touch the stage focus knob.

3. Completely open the Condenser Aperture and completely close the Field Aperture (Fig. 2B).

4. Focus the edges of the Field Aperture by cranking the condenser up or down using the condenser focus knob. Double check that the specimen and the Field Aperture are in focus simultaneously

(Fig. 2C).

5. If the Field Diaphragm is off center, use the two adjusting screws to center the condenser so that the diaphragm image is exactly centered in the field of view (Fig. 2D).

6. Open the Field Diaphragm until its shadow just disappears from the field of view (Fig. 2E).

Opening the Field Diaphragm more than that causes extra glare and decreases image contrast.

Figure 2: Köhler illumination – Focusing and centering the condenser Field Diaphragm

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A: Focus the specimen

B: Field Diaphragm closed down, not focused, not centered

C: Field Diaphragm focused, not centered

D: Field Diaphragm focused and centered

E: Field Diaphragm opened just enough to disappear from view

Microscopy and Imaging Center, Texas A & M University http://microscopy.tamu.edu

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Differential Interference Contrast (DIC, a.k.a. Nomarski) observations

Set up Kohler illumination first.

Make sure the polarizer in the condenser is engaged

Check that the Filter set selected in the software is DIC.

The slider with Nomarski prism below the objective needs to be in the optical path (pushed in).

The

“hockey stick” handle on the slider should be set according to the objective used: pulled out for dry objectives, pushed in for immersion objectives.

(Explanation: This handle controls the distance of the Nomarski prism from the flange of the objective. Dry and immersion objectives have their back focal plane at a different position, The Nomarski prism must be close to the BFP for best performance.)

If the objectives are switched using the software’s pre-set group, the correct Nomarski prism is automatically engaged (and the objective turret retracts before turning to prevent damage or contamination of the objectives).

If you use the buttons on the keypad and on the microscope to switch objectives, you have to manually switch to the correct Nomarski prism in the condenser turret.: Each objective requires a different condenser prism for DIC to work. See table 1 below. Use the control keypad to turn the condenser turret

(two buttons on the keypad, labeled “GFP” and “Cy3”).

Table 1: Condenser turret positions for DIC observation with individual objectives

Objective

UPLSAPO 10x/0.4 dry

Condenser turret position

“hockey stick” handle position on the

DIC objective prism

5

OUT

5

UPLSAPO 20x/0.7 dry

UPLSAPO 40x/0.9 dry

OUT

OUT

2

4

UPLSAPO 60x/1.2 water imm

UPLSAPO 100x/1.4 oil imm

UPLSAPO 20x/0.85 oil imm.

6

5

IN

IN

IN

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Using the 20x and 40x dry objectives- how to keep them clean:

If the slide is clean and does not have any immersion oil, you may switch to the 20x or 40x dry objective. To do so, press the "ESC" button on the microscope (green button behind the focusing wheel) - this retracts the objective turret to prevent damage or contamination of the objectives.

Then use the control keypad to switch to the desired objective and push the "Esc" button again to return to the focus position. You should need only minimal re-focusing (1/4 or 1/2 turn of the focus wheel).

Beware that if your slide already has immersion oil on it, switching to the 20x or 40x objectives will get oil on these dry lenses and will require their careful cleaning by the MIC staff. If this happens, please let the MIC staff know and do not try to clean the lenses yourself. The front lens elements are very delicate and prone to scratching, which would ruin the optics.

Using and cleaning the oil immersion objectives:

Remove the sample from the microscope

Select the “100x oil” or “20x oil” objective in the software

Apply a small drop of immersion oil on the objective

Press the ESC button on the microscope to lower the objective

Put the sample (slide) on the microscope stage in the same orientation as it was before.

Press the “ESC” button to bring the objective into focus

CLEANING

NEVER USE KIMWIPES OR OTHER TISSUE PAPER TO CLEAN OBJECTIVES. USE

ONLY LENS PAPER (e.g. Fisher 11-996)

Using clean lens paper gently blot off the oil from the lens. Do NOT drag the paper across the

lens, just dab off the oil. The front lens of the objective is very delicate and must be protected from scratching.

Wipe off any oil form the objective barrel.

Thorough cleaning of the oil immersion objectives is performed by the MIC staff only.

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Using the 60x/1.2 Water Immersion objective

Remove the sample from the microscope. Make sure the coverslip on your slide is clean and dry, with absolutely no oil

Select the 60x/1.2 water immersion objective in the software

Set the adjustment collar on the objective to the thickness of the coverslip on your specimen

(Coverslips #1.5 are approximately 0.17 mm thick)

Apply a small drop of clean ultra-filtered water on the objective, using a plastic Pasteur pipette

Press the “ESC” button on the microscope to lower the objective turret

Place the sample on the microscope stage in the same orientation as it was before

Press the “ESC” button to bring the objective into focus

CLEANING

NEVER USE KIMWIPES OR OTHER TISSUE PAPER TO CLEAN OBJECTIVES. USE

ONLY LENS PAPER (e.g. Fisher 11-996)

Using clean lens paper gently blot off the water from the lens. Do NOT drag the paper across

the lens, just dab off the oil. The front lens of the objective is very delicate and must be protected from scratching.

Thorough cleaning of the oil immersion objectives is performed by the MIC staff only.

Using objectives with coverslip thickness correction

The dry 40x/0.9 and water immersion 60x/1.2 objectives provide high resolution and good signal intensity only if coverslip of correct thickness is used. These objectives are equipped with an adjustment collar to match the actual coverslip thickness. If the adjustment collar is not properly set, resolution and signal intensity are degraded.

Use coverslips # 1.5 for your specimens. Their thickness is in the 0.16-0.19 mm range, and will vary from batch to batch, and also between individual coverslips. For high-resolution imaging, the objective correction collar must be set to minimize spherical aberration. This setting depends on the coverslip thickness and also on the specimen itself (refractive index, distance from the coverslip).

Microscopy and Imaging Center, Texas A & M University http://microscopy.tamu.edu

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Fluorescence microscopy

Focus on the specimen using transmitted light (DIC), if possible

Switch to the desired filter in the software (e.g., GFP)

Switch from the camera port to eyepiece observation (top left button on the front of the microscope)

Open the mechanical shutter below the objective turret. Illumination light can be attenuated using a lever on the mercury lamp housing

Find and focus the specimen

If you will not be acquiring images right away, close the mechanical shutter or switch beck to

DIC filter set in the software

Beware that the Nomarski prism below the objective degrades the fluorescence image. Thus, if high resolution imaging is needed, pull the Nomarski prism out of the optical path

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CCD camera imaging

Select the desired filter set in the FILTER menu.

Select the desired objective in the OBJECTIVE menu. Take care not to get oil on dry objectives or on the water immersion 60x objective.

Set the Camera Gain

(typically around 8; the higher the gain, the noisier the image)

Binning: 1

Run "Live View" and set the Exposure to get a good image. Optimize the exposure and gain.

Adjust contrast by moving the Min and

Max sliders below and above the histogram or select “Autostretch”.

Switch to the next filter and optimize exposure time as needed.

To set up Multidimensional Acquisition, click the

“Multi-D Acq” button

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Multidimensional Acquisition

Set parameters as needed:

Time Points (1 if not doing time lapse)

Multiple Positions (XY): you can mark XY positions or define a matrix of XY coordinates

Slices (Z) if doing z-stacks; set z-start, z-end and z-step (see Table 2 for optimal z-steps).

Channels: set the filter, exposure time, z-offset

(to correct for focus shift between different colors) and check whether to acquire the channel for every slice in a z-stack or just once.

You can also set to skip a number of frames in a time lapse series.

Assign a name to the experiments (directory and name prefix). Make sure "Save image files to acquisition directory" is checked.

Select the acquisition order (e.g., Channels, slices, time points)

If you want to use the same settings as for images previously saved, in the Multi-D

Acquisition click the Load button to open "Acquisition.xml file from an existing image folder.

Make sure to modify the “Save Images” settings so that the new data files have the proper name and destination. After you set up the acquisition parameters, you can save the settings (”Save

As” button) for future use.

Microscopy and Imaging Center, Texas A & M University http://microscopy.tamu.edu

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XY Pixel size, Recommended Z-step, Sampling and Nyquist Criterion

The Rolera CCD camera has pixels 12.7 µm in size. This provides very good sensitivity, but may limit the spatial resolution. To capture the image at full resolution, the smallest resolved detail in the primary image should be represented by at least two pixels (“Nyquist criterion”).

Each configuration file may contain spatial calibration for each objective. So as long as you switch the objectives using the button in the software, rather than using the keypad by the microscope, the pixel size is known. However, in most user’s config. Files, the calibration is only valid with the 1x field lens on the microscope (the handle on the right side of the microscope below the objective turret is pushed in). When additional magnification is introduced by engaging a 1.6x field lens (the handle on the microscope is pulled out), the sampling is closer to Nyquist criterion, but the calibration is no longer valid. Thus, the automatic generation of multiple XY positions (a matrix of adjacent images) will not work correctly. Images will have to be spatially calibrated after acquisition if measurements are to be done.

If this is a problem and you will be imaging using the additional 1.6x magnification , you can change the spatial calibration (pixel size for each of the objectives) in your config file to the 1.6x field lens values. See table 2 below. You could then save a copy of your configuration file.

Table 2 shows the pixel and resolution calculation. XY resolution is calculated as D

xy

=0.61*

/NA



Axial resolution is calculated as

D z

=1.4·

·

/(NA

2

), where NA is the numerical aperture of the objective,

is the wavelength of signal (here, assumed 500 nm, i.e., 0.5 µm) and

 is the refractive index of the immersion medium (air, 1.0; water, 1.33; oil, 1.515).

Table2. Pixel size for Qimaging Rolera XR camera on Olympus IX81 microscope.

Resolution is calculated for 500 nm wavelength. Green fill indicates that the XY pixel size satisfies the Nyquist criterion. All other conditions result in undersampled images

Objective

10x/0.4 dry

10x/0.4 dry

20x/0.7 dry

20x/0.7 dry

40x/0.9 dry

40x/0.9 dry

60x/1.2 WI

60x/1.2 WI

20x/0.85 oil

20x/0.85 oil

100x/1.4 oil

100x/1.4 oil

NA Imm.

Medium RI

0.4

0.4

0.7

0.7

0.9

0.9

1.2

1.2

0.85

0.85

1.4

1.4

60X/0.7 dry, LWD 0.7

60X/0.7 dry, LWD 0.7

1.00

1.00

1.00

1.00

1.00

1.00

1.00

1.00

1.33

1.33

1.515

1.515

1.515

1.515

Tube

Lens

1x

1.6x

1x

1.6x

1x

1.6x

1x

1.6x

1x

1.6x

1x

1.6x

1x

1.6x pixel size Calc.

[

 m]

D

XY

[

 m]

1.683

0.804

0.763

0.763

0.641

0.401

0.318

0.198

0.214

0.135

0.636

0.399

0.129

0.081

0.221

0.138

0.436

0.436

0.436

0.436

0.339

0.339

0.254

0.254

0.359

0.359

0.218

0.218

Calc.

D

Z

[

 m]

4.38

4.38

1.43

1.43

0.86

0.86

0.65

0.65

1.47

1.47

0.54

0.54

1.43

1.43

Suggest. z-step

Dz/2.3

[

 m]

1.90

1.90

0.62

0.62

0.38

0.38

0.28

0.28

0.64

0.64

0.24

0.24

0.62

0.62

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Data management and conversion

15

Storing your data

The imaging computer is not for long-term data storage. After copying your files to your storage medium and confirming they are OK, erase the files from the computer. Old data files will be purged periodically.

If using CDs or DVDs, store the disks in protective cover in a cool, dark place – the CD-burning layer is heat and light sensitive (after all this is how the data is recorded).

Always create two copies of the data files, store them in different locations, e.g. one in the lab, the other one at home.

Avoid using acidic markers (Sharpie) for labeling disks. Use a non-acidic archival felt-tip marker

Most CDs and DVDs are not an archival medium; they can decay and be unreadable in few years, especially if not stored properly.

Viewing and processing the image files

Recent versions of Micromanager allow saving multi-dimensional data (time-lapse, z-stack, multi-channel) either as individual images (one tiff file for each channel, z-position, time-point) or as a single multi-image TIFF file. This multi-image TIFF file also contains all the metadata in the file header. The best way to open these images is to download and install MicroManager on your computer ( http://www.micro-manager.org

).

The multi-file data can also be opened using ImageJ and the micromanager file opener plugin

(download from micromanager web site).

Data Conversion

ALWAYS KEEP THE ORIGINAL DATA!

If you choose to save the images a multiple files, MicroManager saves data in Image5D format. For each image (or image stack), a new folder is created, named with the

“Name Prefix" set during acquisition in Micromanager. In this folder, the images from each channel and each z-position are saved as 16-bpp grayscale TIF files. In addition, the Metadata are saved as a text file. The imaging parameters and settings are also saved, in the “Acquisition..xml” file.

Acquisition..xml img_000000000_GFP_000.tif img_000000000_GFP_001.tif img_000000000_GFP_002.tif img_000000000_GFP_003.tif img_000000000_GFP_004.tif metadata.txt

To make image browsing and sharing easier, you could export the acquired images and rename them so that the file name contains the name of the sub-folder (= the

“Name Prefix" set during acquisition in Micromanager. Please note that conversion to other formats can result in

images with only 8bits per pixel and/or information loss due to compression, so analysis

and processing should be done on the original files, not the converted ones. Here is how to do the conversion:

Microscopy and Imaging Center, Texas A & M University http://microscopy.tamu.edu

Start IrfanView

"Select File - Batch conversion/rename"

Browse to the folder containing the individual sub-folders with images

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Select "Include Subdirectories"

Set Output Directory to a safe location (e.g., "c:|temp|2012-07-22-exported"). Be careful as not to accidently overwrite your original files.

Select "Batch conversion - Rename result files

Select Output Format (JPG is OK for browsing and emailing)

Set name pattern $d-$F## (incorporates the folder name in the new image name)

If necessary, use the batch Rename Options

Click "Add all"

click "Start"

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SHUTDOWN PROCEDURE

Remove specimen from the stage

Using lens paper only, gently blot excess oil from the oil immersion objective. Do not wipe the lens. NEVER USE KIMWIPES or other kinds of paper on the objective lens. The front lens is easily scratched. Thorough cleaning of the objectives is done by the MIC staff only.

Switch to the lowest magnification objective (10x).

Clean the work area.

Turn off all control boxes and the computer, the Mercury lamp power supply is the last to be turned off.

If you are the last user for the day, and if the lasers are still running, it is your responsibility to turn the lasers off!

Laser turn off procedure:

1. 405 nm diode lasers: turn the key to OFF, turn the power switch to OFF.

2. Red and green HeNe lasers

– turn the knob to OFF

ONLY IF YOU ARE THE LAST

USER FOR THE DAY

3. Argon laser: TURN OFF ONLY IF YOU ARE THE LAST USER FOR THE DAY. IF

NOT, LEAVE THE ARGON LASER RUNNING. i. ii.

Turn the key to OFF position

WAIT!! The laser must cool down.

The fan to stop automatically when the laser unit has cooled down. It takes several minutes iii. Set the power switch to OFF.

Sign off in the log book.

Turn the lights off; make sure the door is locked when you leave.

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