Détector
- Zeiss AxioCam MR R3 CCD Camera 1388 x 1040 pixels, 12-bit, 13 images/s at full resolution, detector size 8.9 mm x 6.7 mm

Tabs Container

id	Instrument Tabs
title	Zeiss Axio-Observer Z1
direction	horizontal

X-Cite 120Q Brochure (pdf)
X-Cite 120Q quick start guide (pdf)
X-Cite 120Q user guide (pdf)
Comparison between mercury and X-Cite emission spectra (Source)

Tabs Page

id	Description
title	Description

Zeiss Axio-Observer Z1 inverted microscope

Roger Gaudry Building, Room R-421

Access upon request to the platform manager. Consult the

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and

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of the

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.

Simple Microscope usage price

Instrument awarded to Dr. Audrey Claing and Jean-Philippe Gratton by the Canadian Foundation for Innovation (CFI)

Applications
- Bright-field
- Phase contrast
- Fluorescence
Light sources
- LED lamp for transmitted light
- X-Cite 120Q 100 W (350~600nmColibri 7 (385/469/555/631) for fluorescence
  Développer
  title

X-Cite complete specifications

- Full specifications of the Zeiss Colibri 7 light source
  Emission peak (nm)
  Power (mW)

334

- 385/30

7

- 150

365

- 469/38

45

- 110

405

- 555/30

34

- 40

436

- 631/33

43

546

37

579

26

50

Information Zeiss Colibri 7

Objectives

2.5x/0.085 Air WD 8.8
Empty
10x/0.25 Air Ph1 WD 6.5
Empty
20x/0.5 Air Ph2 WD 2.0

40x/0.95 Air WD 0.25

Développer

title	Objectives complete specifications

Position	Name	Brand	Full name	ID	Magnification	Numerical Aperture	Immersion	Type	Working distance (mm)	Transmittance (% [nm])	Technique	Cover glass thickness (mm)
1	20x/0.5 Air	Zeiss	20x/0.50 Ph2 EC Plan-Neofluar M27	420351-9910	20x	2.0	Air	Plan Neofluar	2.0	Not Available	BF, PhC, Fluo	0.17
2	Empty
3	40x/0.95	Zeiss	40x/0.95 Plan-Apochromat Corr M27	420660-9970	40x	0.95	Air	Plan ApoChromat	0.25	>80% [400-840]	BF, Fluo	0.13 - 0.21 Correction ring
4	Empty
5	2.5x/0.085 Air	Zeiss	2.5x/0.085 EC Plan-Neofluar M27	420320-9902	2.5x	0.085	Air	Plan Neofluar	8.8	>95% [400-750]	BF, Fluo	0.17
6	10x/0.25 Air	Zeiss	10x/0.25 Ph1 N-Achroplan M27	420941-9911	10x	0.25	Air	AchroPlan	6.5	Not available	BF, PhC, Fluo	0.17

Filter cubes

DAPI
GFP
Rhodamine
DHE (dihydroethidium)
Cy5

Quadruple DAPI/GFP/Cy3/Cy5

Développer

title	Filters complete specifications

Position	Name	Brand	ID	Excitation filter	Dichroic mirror	Emission filter	Comments
1	DAPI Filter Set 49	Zeiss	488049-9901	365/50 [325-375]	395LP	445/50 [420-470]
2	GFP Filter Set 13	Zeiss	488013-0000	470/20 [460-480]	495LP	517/25 [505-530]
3	Rhodamine Filter Set 43	Zeiss	000000-1114-101	545/25 [533-567]	570LP	605/70 [570-640]
4	DHE	Custom	Custom	500/50 [475-525]	540LP	580/20 [570-590]	Undefined specifications Best guess values
5	Cy5 Filter Set 50	Zeiss	488050-9901	640/30 [625-655]	660LP	690/50 [665-715]
6

1. Quadruple
  DAPI/GFP/Cy3/Cy5
  FS90 HE LED
  489090-9110-000
  
  QBS 405 + 493 + 575 + 653
  QBP 425/30+514/30+592/25+709/100
  Excitation filters included in the light source FS90 HE LED

Detector

Empty

Tabs Page

id	User Guide
title	User Guide

The X-Cite lamp must be on for at least 30 min before being turned off and vice-versa

for the incubation module (#2A) and open the CO₂ cylinder (#2B)

Turn on the power bar at the left of the computer monitor (#3)

Press the microscope start button located on the rear left of the microscope (#4)

Log in Windows using your UdM credentials

UI Expand

Start-up

expanded	true
title		Startup

Remove the dust cover from the microscope
Turn on the computer (#1)
Turn
If necessary, turn on the microscope power bar (#2)
Press the power witch on the left side of the microscope (#3)

If fluorescence is required, turn on the X-Cite lamp (#4A) and open the diaphragm (#4B)

Avertissement

Remarque
When using for the first time, it is necessary to import the microscope-specific parameters BEFORE starting the software. See the First Use section below.

Start -up Zen Bluethe Zen software

UI Expand

title	First Use

When using for the first time, it is necessary to import the microscope-specific parameters into the software. This procedure is usually carried out during the training session.However, it is also possible to use it to reset the software if it is not displayed correctly, for example.

Remarque
Please note, this procedure will delete all your experiment protocols and restore the software to its original settings.

If open, close the Zen software and wait for it to close completely (up to 30 seconds)
On the Desktop open the Documentation folder
Double-click Settings for Axio-Osberver Z1
A script will run and a black window will appear briefly
You can then reopen the Zen software

Shutdown

UI Expand

title	Loading samples

This procedure puts the microscope in a safe configuration and performs a focus calibration. At the end of this procedure the microscope will be ready for acquisition.

UI Expand

title	Focus Calibration Z

On the microscope touch screen:

Press Home>Load Position to lower the stage to its lowest position
Press Set Work Position to store this position
If necessary, move the focus slightly up to remove the “Lower Z limit reached” message displayed on the touchscreen
Press Home>Microscope>Turret>Objectives>10x to select the 10x objective
If asked, tap Done to remove the oil lens cleaning warning
Press Home>Microscope>XYZ>Position>Z-Position>Set zero>Auto to perform focus calibration
Press OK to start the focus calibration procedure
Wait a few seconds for the calibration to be completed

Remarque
Once calibrated, the focus can be found at Z = 1.5 mm). The Z value can be found on the microscope touch screen Home>Z-Position

Info

The first time you use the instrument, you need to import the microscope settings into the software. To do this follow the instructions Software setup.

UI Expand

title	First focus

Avertissement

Save your data
Close Zen Blue
Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive
Turn off the computer
If fluorescence was used, turn off the X-Cite lamp (#4A)
Turn off the microscope power bar (#2)
Cover the microscope

title	Important

Make sure to calibrate the focus before performing the first focus.

On the microscope touch screen:

Press Home>Microscope>Turret>Objectives

Press 10x to select the 10x lens

Info
The 10x objective is the safest because it has the longest working distance (6.5 mm). The sample will appear perfectly sharp long before the lens approaches it. It is recommended to always first focus with the safest lens. The objectives are para-focal, focusing with the safest objective will then allow you to easily find your sample with another objective.

Press Home>Load Position to lower the stage to its lowest position
Press Set Work Position to store this position
If necessary, move the focus slightly up to remove the “Lower Z limit reached” message displayed on the touchscreen
Place the test slide on the microscope stage with the coverslip toward the objective
Remarque
title Important
Always use the test slide to perform the first focus.
If necessary, move the stage so that the sample is centered on the objective

On the computer:

Open the Zen software
In the Locate tab, select BF or the desired fluorescence (GFP, DsRed, DAPI, etc…) to activate the configuration
Adjust the focus with the main dial while looking through the eyepieces until the image is perfectly sharp

Remarque
Once calibrated, the focus can be found at Z = 1.5mm). The Z value can be found on the microscope touch screen Home>Z-Position
In the Locate tab, select Off to turn off the illumination

UI Expand

title	Seconday focus

Avertissement

title	Important

First focus with the safest lens before selecting another lens and continuing with secondary focus.

UI Expand

title	Focusing with air objectives

After performing the first focus, on the microscope touch screen:

Press Home>Microscope>Turret>Objectives

Press 20x or 40x to select the desired lens

Info
The 40x objective is the best Air objective because it has the greatest number of optical corrections (Plan Apochromat) and the largest numerical aperture (0.95). It offers a lateral resolution of 420nm at a wavelength of 550nm.

Adjust the focus with the precision dial while looking through the eyepieces until the image is perfectly sharp
Your sample is ready for acquisition!

UI Expand

title	Focusing with oil lenses

This microscope does not have oil immersion objectives. However, if there were, the procedure would be as follows:

After performing the first focus, on the microscope touch screen:

Press Home>Microscope>Turret>Objectives

Press 63x Oil, 100x Oil (1.3) ou 100x Oil (1.4) to select the desired lens. The microscope will automatically lower the stage so that the sample is accessible.

Info
The 63x objective is the best oil objective because it has the most optical corrections (Plan Apochromat) and the largest numerical aperture (1.4). It offers a lateral resolution of 240nm at a wavelength of 550nm.

Place a drop of oil on your sample
Press Done. The microscope will automatically return the sample to its original position

In Zen Blue software:

In the Locate tab, select BF or the desired fluorescence (GFP, DsRed, DAPI, etc…) to activate the configuration
Adjust the focus with the precision dial while looking through the eyepieces until the image is perfectly sharp
In the Locate tab, select Off to turn the illumination off
Your sample is ready for acquisition!

Remarque

title	Important Reminders

Take back your samples including ones in the microscope

Leave the microscope and the working area clean

The X-Cite lamp must be on for at least 30 min before being turned off and vice-versa

UI Expand

title	Storage management

Files can be saved saved temporarily (during acquisition) on the local C: drive (desktop)
At the end of each session, copy your data to your external drive and delete it from the local C: drive
You can store your files on the D: drive (Data Storage). If you do, please create a folder per laboratory using the principal investigator last name. Within, create one folder per user (Firstname_Lastname).

Remarque
In any case, your files should be removed from the C: drive.

UI Expand

title	Software setup		Shutdown

Save your data
Close the Zen software
Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive
If used, turn off the incubation module power strip (#2A) and close the CO₂ cylinder (#2B)
Select the 10x objective and press load position to bring the objectives to the bottom position
Turn off the microscope power bar (#3)
Turn off the computer
Cover the instrument with the protective dust cover

Remarque

title	Important Reminders

Take back your samples including ones in the microscope
Leave the microscope and the working area clean

The first time you use the instrument, you need to import the microscope settings into the software. You will usually do this during the training session.
This procedure can also be performed if something is not working properly and if you want to reset the software to its original settings.

Remarque
This process will delete all experiment protocols and reset the software to the original settings for this specific microscope.

If open, close Zen Blue and wait until it is completely closed (up to 30 seconds)

On your Desktop open the Documentation folder

Double click on Zen Settings for Axio-Observer Z1

You can now reopen Zen Blue

Tabs Page

id	Lightpath
title	Lightpath

The following schematics depict the light path for transmitted (bright-field and Phase Contrast) and reflected (fluorescence) lights.

PDF

name	LightPath_Zeiss

Axio-Observer Z1 Lightpath (pdf)

_Z1.pdf

Tabs Page

id	Manuals
title	Manuals

Available manuals

Tabs Page

id	Log
title	Log

UI Expand

title	To do

Check stage tilt
Ask for Colibri Remote
Ask for fluorescence backlight from LED

UI Expand

title	2024-02-22 Microscope Firmware update

Microscope Firmware update to add Colibri to the touchscreen
Zen 3.5 HotFix 10

UI Expand

title	2022-05-09

Computer replacement
Added Colibri
Added startup procedure
Parafocality and paracentralityNothing

UI Expand

title	2022-03-17

Added complete description

UI Expand

title	2021-09-27

Added to wiki

Tabs Page

id	Technical Datasheet
title	Technical Datasheet

Stand

Zeiss Axio-Observer Z1 inverted Serial: 3851001242 Part Number: 431007-9902-000
System ID: 1024979772
Camera adapter Model 60N-C, 1", 1x, Model: 426114

Light sources

Transmitted LED light
TBD Filters

X-Cite 120Q Serial: TBD

Colibri 7 R(G/Y)B-UV 423052-9730-000 Serial 5440000661

Condenser

Manual condenser Product number: TBD, Serial: TBD
Lens NA 0.35 WD 70 mm Part Number: 424241
Filter turret 6 positions manual
1. H
2. Ph0
3. Ph1
4. Ph2
5. DIC
6. DUC

Objectives

2.5x/0.085 Air WD 8.8
Empty
10x/0.25 Air Ph1 WD 6.5
Empty
20x/0.5 Air Ph2 WD 2.0
40x/0.95 Air WD 0.25

Stage

Motorized stage Marzhauser Sensotech, Part number 432903-9011-000, #14 07 132052; 90-76-200-0820
Remote control joystick
Inserts
- Slide combo
- 6-well plate
- 35 mm dish
- Multi-well plat

Filters

DAPI Filter Set 49
GFP Filter Set 13
Rhodamine Filter Set 43
DHE (dihydroethidium) 424931
Cy5 Filter Set 50Empty
Multiband FS90 HE LED

Detector

Zeiss AxioCam MR R3 CCD Camera 1388 x 1040 pixels, 12-bit, 13 images/s at full resolution, detector size 8.9 mm x 6.7 mm. Model: r3.1 Part Number: 426509-9901-000. Serial: 1 22 12 5537

Workstation

Fujitsu Esprimo P920 E90+
Intel Core i5-4670 @ 3.4 GHz
RAM 32 GB DDR3 1600 MHz ECC (4 x 8 GB)
OS 500 GB SSD 550 MB/s
2 TB HD Data Storage (2 x 1 TB spanned volume) 110 MB/s
Video Card AMD FirePro V4900 1 GB DDR5 dedicated memory
Monitor TBD display TBDMonitor LG Flatron E2711 27' 1920 x 12001080
Software Zen Blue 2.03.5 HASP YRMDZ 1798977001 1798977001

Incubation

Pecon stage top incubationTBD

Consumables

CO₂ Tank
N₂ Tank
Liquid Light Guide
Oil
Lens Cleaner100 W Mercury lamp

Tabs Page

id	FAQ
title	Troubleshooting & FAQ

Troubleshooting

UI Expand

title	I don't see any fluorescence!see a high background in fluorescence

The fluoresncece light source is a Colibri while the transmitted light is a LED. What happens is that the fluorescence illumination reflects and into the LED and give a high background. To solve this:

Tilt the transmitted light arm backward
or
Stop the light from entering the transmitted LED by using a cardboard

This microscope is motorized for most of its components, yet the X-Cite light source is manual. Ensure the X-Cite diaphragm (#4B) fully opened (high position).

On the X-Cite lamp

Turn the intensity diaphragm (#4B) up

FAQ

UI Expand

title	Can I use this microscope to look at cell in a dish?

Yes. This is an inverted microscope designed to look at specimen in a dish or a multi-well plate
The objectives are optimized to image through thin glass bottom multi-well plates
You may also image specimen mounted between a slide and a 0.17mm thick coverslip
For long timelapse, be aware of photo-toxicity

UI Expand

title	Can I use this microscope to perform timelapse experiments?

Yes, but... This microscope has an incubation module to maintain temperature, humidity and gas. Yet it does not have a Definite focus which can maintain focus throughout time. Therefore, it is possible to loose the focus over long period.

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id	Demo Image
title	Zeiss Axio-Observer Z1
direction	horizontal

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id	Demo Image
title	Demo Image

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Zeiss Axio-Observer Z1 inverted microscope

Stand

Light sources

Condenser

Objectives

Stage

Filters

Detector

Workstation

Incubation

Consumables

Troubleshooting

FAQ

Raccourcis espace

Arborescence des pages

Historique de la page

Comparaison des versions

Ancienne version 18

Nouvelle version Actuel

Légende

Zeiss Axio-Observer Z1 inverted microscope

Stand

Light sources

Condenser

Objectives

Stage

Filters

Detector

Workstation

Incubation

Consumables

Troubleshooting

FAQ