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icon	build
title	Français
type	primary
url	https://wiki.umontreal.ca/display/Microscopie/Zeiss +Axio-Observer+Z1

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id	Instrument Tabs
title	Zeiss Axio-Observer Z1
direction	horizontal

Tabs Page

id	Description
title	Description

Zeiss Axio-Observer Z1 inverted microscope

Roger Gaudry Building, Room R-421

Z1 Colibri

Zeiss Z1-Colibri Microscope

Desmarais Building, Room 2234
Simple Microscope usage price
Instrument awarded to Dr. Audrey Claing and Dr. Jean-Philippe Gratton by the Canadian Foundation for Innovation (CFI) in 2014

Applications

Inverted microscope
Widefield imaging
Brightfield

Bright-field

- Phase contrast
- Fluorescence
Incubation
Timelapse imaging
Deconvolution
Extended Depth of Focus

Image Added

Tabs Container

direction	horizontal

Tabs Page

id	Description
title	Description

Description

Light sources

LED lamp for transmitted light
Colibri 7

(385

R[G/Y]B-UV (385/469/555-590/631) for fluorescence

Expand

title

Full specifications of the Zeiss Colibri 7 light source

Complete specifications

Emission peak (nm)	Nominal Power (mW)	Measured Power (mW)
385/30	150
469/38	110
555/30	31

32Information

631/33

52

50

View file

name	Zeiss_Colibri-7_Product Information.pdf
height	250

Image Added

Objectives

20x10x/0.25 Air Ph1 WD 6.5

2.5x/0.

5 Air Ph2 WD 2.0

Empty

63x/1.4 Oil DIC WD

Empty

2.5x/0.075 Air WD 2.0

075 Air
10x/0.25 Air Ph1
20x/0.5 Air Ph2
40x/0.75 Air Ph2
63x/0.75 Air Ph2 Long Distance
63x/1.4 Oil

Expand

title

Objectives complete

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

2.5x/0.

5

075 Air

Zeiss

20x

2.5x/0.

50 Ph2420351

075
EC Plan-Neofluar

M27

420320-

9910

9901-000

20x

2.5x

0.075

Air

Plan

-

Neofluar

2

9.

0

5	>80% [400-

800

840]

BF

, PhC

, Fluo	0.17
2

Empty

363x/1.4

10x/0.25 Air

Zeiss

63x

10x/

1

0.

4

25 Ph1

Plan

N-

Apochromat Oil
M27

Achroplan

420941-9911

420782-9900

-000

63x

10x

1

0.

4

25

Oil

Air

Plan Apo

N-

chromat

AchroPlan

0

6.

19>80% [450-750]

5

Not Available

BF, PhC, Fluo

0.17

4Empty5

3

20x

2.5x

/0.

075

5 Air

Zeiss

2.5x

20x/0.

075420320-9901

50 Ph2
EC Plan-Neofluar

M27

420351-9910-000

2.5x

20x

0.

075

50

Air

Plan

-

Neofluar

9

2.

5>90% [400-750]

0

Not Available

BF, PhC, Fluo

0.17

6

4

10x

40x/0.

25

75 Air

Zeiss

10x

40x/0.

25 Ph1
N-Achroplan
M27

75 Ph2
EC Plan-Neofluar

420361-9910

420941-9911

-000

10x

40x

0.

25

75

Air

AchroPlan

Plan Neofluar

6

0.

5>80% [400-800]

71

Not Available

BF, PhC, Fluo

0.17

Filter cubes

DAPI

GFP

DsRed

DHE (dihydroethidium)

Cy5

Quadruple DAPI/GFP/Cy3/Cy5
Expand

title	Filters complete specifications

PositionNameBrandIDExcitation filterDichroic mirrorEmission filterComments1DAPI
Filter Set 49Zeiss

488049-9901

365/50
[325-375]395LP445/50
[420-470]2GFP
Filter Set 13Zeiss488013-0000

470/20
[460-480]

495LP

517/25
[505-530]3DsRed
Filter Set 43Zeiss

000000-1114-101

545/25
[533-567]570LP605/70
[570-640]4DHECustom

Custom

500/50
[475-525]

540LP580/20
[570-590]Undefined specifications
Best guess values5Cy5
Filter Set 50Zeiss488050-9901640/30
[625-655]660LP

690/50
[665-715]

6Quadruple
DAPI/GFP/Cy3/Cy5
FS90 HE LED489090-9110-000
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
- 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 Page

id	User Guide
title	User Guide

UI Expand

expanded	true
title	Startup

Remove the dust cover from the microscope
Turn on the computer (#1)
If necessary, turn on the power bar 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
Note
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 the 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.

5

63x/0.75 Air

Zeiss

63x/0.75 Corr Ph2
LD Plan-Neofluar

421381-9970-000

63x

0.75

Air

LD Plan-Neofluar

1.7 at cover glass 0.75

Not Available

BF, PhC, Fluo

0 - 1.5

6

63x/1.4 Oil

Zeiss

63x/1.4 DIC
Plan-Apochromat Oil

420782-9900-000

63x

1.4

Oil

Plan Apochromat

0.19

>80% [400-700]

BF, Fluo

0.17

Filter

DAPI
GFP
Rhodamine
DHE (dihydroethidium)
Cy5
Quadruple DAPI/GFP/Cy3/Cy5

Expand

title	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	DsRed 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	Quadruple DAPI/GFP/Cy3/Cy5 FS90 HE LED	Zeiss	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

Detectors

PCO Edge 5.5

Expand

title	Complete specifications

Camera	PCO Edge 5.5
Sensor Type	sCMOS
Sensor Category	Monochrome
Nb Pixels	5.5 M
Pixel Layout	2560 x 2160
Pixel size	6.5 um
Sensor size	16.6 mm x 14.0 mm
Sensor diameter	21.8 mm
Bit depth	16-bit
Speed at full resolution	100 images/s
Max QE	60 % at 600 nm
Reading noise	1.0 e⁻
Cooling	Forced air +7C
Dark Current	0.6 e⁻/pixel/sec
Full well capacity	30 000 e-
Dynamic Range	1:30000
Interface	Dual Camera Link PCIe
Mount	C-mount

Image Added

View file

name	PCO_Edge 5.5_Datasheet.pdf
height	250

Zeiss Axiocam MRm (not installed)

Expand

title	Complete specifications

Camera	Zeiss Axiocam MRm
Sensor Type	CCD
Sensor Category	Monochrome
Nb Pixels	1.4 M
Pixel Layout	1388 x 1040
Pixel size	6.45 um
Sensor size	8.9 mm x 6.7 mm
Sensor diameter	11 mm
Bit depth	12-bit
Speed at full resolution	13 images/s
Max QE	55 %
Readout noise	8 e⁻
Cooling	Pelletier
Dark Current	0.7 e⁻/pixel/sec
Full well capacity	17 000 e-
Dynamic Range	1:2000
Interface	FireWire (IEEE 1394a)
Mount	C-mount

Image Added

View file

name	Zeiss_AxioCam MRm_Datasheet.pdf
height	250

Tabs Page

id	User Guide
title	User Guide

User Guide

UI Expand

expanded	true
title	Startup

If not already done, turn on the computer (#1) and log in to Windows using your UdeM credentials
Remove the dust cover from the microscope
If incubation is required, turn on the incubation power bar (#2) on the desk near the computer and open the CO₂ cylinder (#2B) near the sink
Note
Make sure the humidifier is properly filled with distilled water.
Turn on the microscope power bar (#3) on the desk near the computer
When using the instrument for the first time, it is necessary to import the microscope configuration before starting the software. See the First Use section below.
Start Zen

UI Expand

title	First Use

When using the instrument for the first time, it is necessary to import the microscope configuration into the software. This procedure is usually carried out during the training session. However, it can also be used to reset the software if it does not display correctly, for example. Running this procedure will erase all your experiment protocols and reset the software to its original settings (ask for support if you are not sure).

If Zen is open, close it and wait until it has completely shut down (this may take up to 30 seconds)
On the Desktop, open the Softwares folder
Double-click Zen Settings for Zeiss Z1-Colibri
A script will run and a black window will appear briefly
When the message Settings for Zen have been imported successfully appears, click OK to close it
You can now open Zen

UI Expand

title	Loading samples

During this procedure, you will:

Set the microscope to a safe configuration
Perform a calibration
Load your sample
Find and adjust the focus

Once completed, your sample will be ready for acquisition.

UI Expand

title	Calibration

This step is required to calibrate the microscope in XY and Z. Performing this calibration will significantly reduce the time needed to locate and focus on your sample.

If not already done, select the lowest-magnification objective. On the microscope touch screen Home > Microscope > Control > Objectives > 2.5x
In Zen, once it has started a calibration dialog should appear. Simply click Calibrate Now.
The microscope will lower the objectives, perform an XY calibration first, followed by a Z calibration, and then return to its original position.

Tip
Once calibrated, the focus is typically found at Z = 1.1 mm for a microscope slide. For a multi-well plate the focus is generally around Z = 3 mm but this is highly dependent on your multi-well plate. The Z position can be viewed on the microscope touch screen under Home > Z-Position, as well as in Zen within the Focus tab, located on the right side of the screen.

Expand

title	The calibration dialog did not appear...

The system may already be calibrated. This can occur if a previous user calibrated the system and left it on.

UI Expand

title	Verifying if the system is already calibrated

In Zen, within the Focus tab, located on the right side of the screen:

Click Load to lower the objective
The Z position is indicated below Current
If Z position value is less than 100 um the system is calibrated

On the microscope touch screen:

Lower the objective by pressing Home > Load Position
Press Set Work Position to store this position
If necessary, slightly adjust the focus upward to clear the Lower Z Limit Reached message displayed on the touch screen
The Z position value is indicated
If the value is less than 0.1 mm then the system is calibrated

UI Expand

title	Manual calibration with the software

In Zen, within the Stage tab, located on the right side of the screen:

If not already done, check the Show All option
At the bottom of the tab click Calibrate
A warning message will show up click Continue
The microscope will lower the objectives and perform a XY stage calibration and then return to its original position.

In Zen, within the Focus tab, located on the right side of the screen:

If not already done, check the Show All option
At the bottom of the tab click Calibrate
A warning message will show up click Continue
The microscope will then perform a Z calibration and then return to its original position

XY and Z calibrations are now complete

UI Expand

title	Manual calibration with the microscope touch screen

On the microscope touch screen:

Navigate to Home > Microscope > XYZ > Position > Z-Position > Set Zero > Auto to perform focus calibration
Press OK to start the calibration procedure
Wait a few seconds for the calibration to complete
Lower the objective by pressing Home > Load Position

Note
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

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

slightly adjust the focus

slightly up

upward to

remove

clear the

“Lower

Lower Z

limit reached”

Limit Reached message displayed on the

touchscreen

touch screen
Navigate to Home > Microscope > XYZ > Position > XY-Position > Set Zero > Auto to perform a stage

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 NoteOnce 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

the calibration to complete

XY and Z calibrations are now complete

UI Expand

title	Ensuring the calibration dialog is displayed at startup

In Zen:

In the menu bar, navigate to Tools > Options
Select Startup/Shutdown
Under Stage/Focus Calibration, ensure Request Stage/Focus Calibration on Startup is checked
Click OK to close the Options dialog

UI Expand

title

First

Initial focus

Warning

title	Important

Make sure to calibrate the focus before performing the first focusPress 10x to select the 10x lens

Ensure that the calibration has been completed beforehand. Calibration will significantly reduce the time required to locate and focus on your sample.

On the microscope touch screen:

Press Home>Microscope>Turret>Objectives

If not already done, select the lowest-magnification objective Home > Microscope > Control > Objectives > 2.5x

Info
The

10x objective is the safest because it has the longest

2.5× and 10× objectives are the safest to use due to their long working distance (

6.5

>6 mm). The sample will appear

perfectly

in sharp

long

focus well before the

lens

objective approaches it. It is recommended

to always first

to always focus

with

using the safest

lens

objectives first.

The

Since the objectives are

para-focal

parafocal, focusing with the safest

objective will then allow you to easily find your sample with another objective.

objectives will facilitate locating the sample when switching to higher-magnification objectives.

Lower the objective by pressing Home > Load Position

Press Home>Load Position to lower the stage to its lowest position

Press Set Work Position to store this position
If necessary,

move

slightly adjust the focus

slightly up

upward to

remove

clear the

“Lower

Lower Z

limit reached”

Limit Reached message displayed on the

touchscreen

touch screen
Place the test slide on the microscope stage with the coverslip

toward

facing the objective
Note
title Important

Always use the

Using a test slide

to perform the first focus

will significantly reduce the time required to set up the instrument.
If necessary,

move

adjust the stage

so

to ensure that the sample is

centered on Open the Zen software

centred under the objective

On the computer:

In Zen:

In

the

the Locate tab, select BF or the desired fluorescence (Fluo, DAPI, GFP,

DsRed

Cy3,

DAPI, etc…

Cy5) to activate the configuration
Adjust the focus with the main dial while looking through the eyepieces until the image is perfectly sharp

note

Info
Once calibrated, the focus

can be

is typically found at Z =

1.5mm). The Z value can be found

1.1 mm for a microscope slide. For a multi-well plate the focus is generally around Z = 3 mm but this is highly dependent on your multi-well plate.
The Z position can be viewed on the microscope touch screen

Home>Z-Position

under Home > Z-Position, as well as in Zen within the Focus tab, located on the right side of the screen.

In the Locate tab, select Off to turn off the illumination

UI Expand

title	Seconday focus

Warning

title	Important

First

Perform the initial focus

with

using the safest

lens before selecting another lens and continuing with secondary focus

objective before switching to higher-magnification objectives.

UI Expand

title	Focusing with air objectives

After performing the

first

initial focus, on the microscope touch screen:

Press

Home>Microscope>Turret>

Home>Microscope>Control>Objectives
Press 10x, 20x

or 40x

, 40x or 63x (0.75) to select the desired

lens

objective

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).

largest Numerical aperture (0.75) together with a wider field of view (40x).

In Zen:

In the Locate tab, select BF or the desired fluorescence (Fluo, DAPI, GFP, Cy3, DsRed, Cy5) to activate the configuration

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
In the Locate tab, select Off to turn off the illumination

Your sample is ready for acquisition!

UI Expand

title	Focusing with oil

lensesThis microscope does not have oil immersion

objectives

. However, if there were, the procedure would be as follows:

After performing the

first

initial 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.

InfoThe 63x objective is the best oil objective because it has the most optical corrections (Plan Apochromat) and the largest numerical aperture

Press 63x Oil (1.4)

.

It offers a lateral resolution of 240nm at a wavelength of 550nm

to select the desired objective. The microscope will automatically lower the stage so that the sample becomes accessible.
Place a single drop of oil on

your sample

the objective
Press Done. The microscope will automatically return the

sample

objective to its original position

In Zen

Blue software

:

In

the

the Locate tab, select BF or the desired fluorescence (Fluo, DAPI, GFP, Cy3, DsRed,

DAPI, etc…

Cy5) to activate the configuration
Adjust the focus with the precision dial while looking through the eyepieces until the

eyepieces until the

image is perfectly sharp
In the Locate tab,

select

select Off to turn off the illumination

off

Your sample is ready for acquisition!

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).

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

UI Expand

title	Shutdown

Save your data

Close the Zen software

Close Zen
Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive
If used, clean oil objectives with lens cleaner and paper
Select the lowest magnification objective and press load position to place the objectives in a safe position
If used, turn off the incubation module power

strip Select the 10x objective and press load position to bring the objectives to the bottom position

strip (#2A) and close the CO₂ cylinder

(#2B)

(#2B)
Turn off the microscope power bar (#3)
Turn off the computer
Cover the instrument with the protective dust cover

Note

title

Important Reminders

Reminder

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

Tabs Page

id

title

Lightpath

Log

titleLightpath

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

PDF

name	LightPath_Zeiss_Z1.pdf

Log

UI Expand

title	To be done

Measure Power output
Modify camera power supply cable

UI Expand

title	2025-10-22 Windows 11 and more

Installation of Windows 11
Added CO2 connection to incubation module
Cable management
Replaced video card

UI Expand

title	2025-09-01 Camera upgrade

Added compressed air connexion to the anti-vibration table

UI Expand

title	2025-09-01 Camera upgrade

AxioCam replacement with PCO Edge 5.5

Tabs Page

id	Manuals
title	Manuals

Available manuals

Tabs PageidLogtitleLog

UI Expand

title

To do

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

2025-08-21 Wiki Updated

Updated wiki with complete specifications

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 paracentrality

UI Expand

title	2022-03-17

Added complete description

UI Expand

title	2021-09-27

Added to wiki

Tabs Page

id

title	Technical Datasheet

title

Technical Datasheet

Stand

Zeiss Axio-Observer Z1

inverted

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

Condenser

Manual

condenser Product number: TBD, Serial: TBDEmpty

condenser
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

075 Air 420320-9901-000

Empty

10x/0.25 Air Ph1

WD 6.5

420941-9911-000

20x/0.5 Air Ph2

WD 2.0

420351-9910-000
40x/0.75 Air Ph2 420361-9910-000
63x

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 50
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+

75 Air Ph2 Long Distance 421381-9970-000
63x/1.4 Oil 420782-9900-000

Stage

Motorized stage Marzhauser Scan IM 130x100-2mm 90-24-550-0000 Serial 16053038
Stage Controller 90-76-024-1803 Serial 14 04 1 2040 SMC 2009 432929-9011-000
Remote control joystick 2-Axis 90-76-200-0820 Zeiss Article 432903-9011-000 Serial 1615142059
Inserts
- Slide combo
- Multi-well plate

Filters

DAPI Filter Set 49 488049-9901
GFP Filter Set 13 488013-0000
Rhodamine Filter Set 43 000000-1114-101
DHE (dihydroethidium) 424931
Cy5 Filter Set 50 488050-9901
Multiband FS90 HE LED 489090-9110-000

Detector

Zeiss AxioCam MRm Model: r3.1 Part Number: 426509-9901-000. Serial: 1 22 12 5537
PCO Edge 5.5 Model pco.API.Air.BX Serial 6000001404

Workstation

Computer
- Fujitsu Esprimo P920 E90+ Model MI5W Serial YLPS036541
Motherboard
- Fujistsu D3222-A1 (1 PCIe Gen3 x16, 1 PCIe Gen 2 x16 (x4 lanes), 2x PCIe Gen2 x1
- Chipset Intel Q87
- BIOS UEFI compatible American Trend v4.6.5.4 R1.47.0 for D3222-A1x 2019-08-26
Processor

- Intel Core i5-4670 @ 3.4 GHz
RAM

32 GB DDR3 1600 MHz ECC (4

- 24 GB DDR3 800 MHz (3 x 8 GB)
OS

500 GB

Drive
- 1 TB SSD 550 MB/s
- Win 11 23H2
Storage
- 2 TB HD

Data Storage (2 x 1 TB spanned volume) Monitor

- 110 MB/s
Video

Card AMD FirePro V4900 1 GB DDR5 dedicated memory

Card
- AMD FirePro V4900 1 GB DDR5 0.768 TFLOPS 1x PCIe gen2 x16
Monitor

- LG Flatron E2711 27' 1920 x 1080
- LG W2442 1920 x1080
Software
- Zen Blue 3.5
- Serial 1121159628-524292
- HASP

YRMDZ 1798977001 1798977001

Incubation

- 1798977001
- Extended Focus
- Measurements
- Multi-Channel
- Panorama
- Software autofocus
- Time Series
- Z-stack

Incubation

Pecon stage top incubation

Anti-vibration table

TMC Model 63 512 Serial 933240
Plain table top

Pecon stage top incubationN

Consumables

CO

₂ Tank

₂ Tank
Oil
Lens Cleaner

Manuals

Tabs Page

id	FAQ
title	Troubleshooting & FAQ

title	Troubleshooting & FAQ

Troubleshooting

UI Expand

title	I don't see any fluorescence!

Technical support is free and unlimited. Contact us !

Troubleshooting

UI Expand

title	I 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

This happens in the following conditions at

At 2.5x using the DAPI or GFP channel
At 10x using the GFP channel
At 20x using the GFP channel

To solve this you can use any of the following option:

Tilt the transmitted light arm backward

or

Close the manual shutter between the condenser and the transmitted light
Use a higher magnification objective

Stop the light from entering the transmitted LED by using a cardboard

FAQ

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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

.

. You can always do a software autofocus at different time but be aware of photo-toxicity if you are using fluorescence.

UI Expand

title	What is Extended Depth of Focus?

Extended Focus is a method to flatten a Z-stack by keeping only the relevant information.

In Zen:

Select the Processing Tab
Select the Extended Depth of Focus Method
Click Apply
Wait until the processing is finished
Save the processed image

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title	Zeiss Axio-Observer Z1
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title	Demo Image

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New Version Current

Key

Zeiss Axio-Observer Z1 inverted microscope

Zeiss Z1-Colibri Microscope

Applications

Inverted microscope
Widefield imaging
Brightfield

Description

Light sources

Objectives

Filter

Detectors

User Guide

Log

Technical Datasheet

Stand

Light sources

Condenser

Objectives

Stage

Filters

Detector

Workstation

Stage

Filters

Detector

Workstation

Incubation

Incubation

Anti-vibration table

Consumables

Manuals

Troubleshooting

FAQ

Space shortcuts

Page tree

Page History

Versions Compared

Old Version 41

New Version Current

Key

Zeiss Axio-Observer Z1 inverted microscope

Zeiss Z1-Colibri Microscope

Applications

Inverted microscopeWidefield imagingBrightfield

Description

Light sources

Objectives

Filter

Detectors

User Guide

Log

Technical Datasheet

Stand

Light sources

Condenser

Objectives

Stage

Filters

Detector

Workstation

Stage

Filters

Detector

Workstation

Incubation

Incubation

Anti-vibration table

Consumables

Manuals

Troubleshooting

FAQ

Inverted microscope
Widefield imaging
Brightfield