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icon	build
title	Français
type	primary
url	Zeiss Z1 Colibri

Lire en Francais

Zeiss

Axio

Z1-

Observer Z1

Colibri

inverted microscope

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

Transmitted light

Applications

Inverted microscope
Widefield imaging
- Brightfield
- Phase contrast
- Fluorescence
Incubation
Timelapse imaging
Deconvolution

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Extended Depth of Focus

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Instrument Tabs

Tabs Container

id

direction	horizontal

auitabspage

Tabs Page

id	Description
title	Description

Description

Light sources

LED lamp for transmitted light
Colibri 7 R[G/Y]B-UV (385/469/555-590/631) for fluorescence

Expand

title	Complete specifications

Emission peak (nm)	Nominal Power (mW)	Measured Power (mW)
385/30	150
469/38	110
555/30	31
631/33	50

View file

name	Zeiss_Colibri-7

Objectives

_Product Information.pdf
height	250

Image Added

Objectives

2.5x2.5x/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	Complete specifications

Position	Name	Brand	Full name	ID	Magnification	Numerical Aperture	Immersion	Type	Working distance (mm)	Transmittance (% [nm])	Technique	Cover glass thickness (mm)
1	2.5x/0.075 Air	Zeiss	2.5x/0.075 EC Plan-Neofluar

M27

420320-9901-000	2.5x	0.075	Air	Plan Neofluar	9.5	>80% [400-840]	BF, Fluo	0.17
2	10x/0.25 Air	Zeiss	10x/0.25 Ph1 N-Achroplan

M27

420941-9911-000	10x	0.25	Air	N-AchroPlan	6.5	Not Available	BF, PhC, Fluo	0.17
3	20x/0.5 Air	Zeiss	20x/0.50 Ph2 EC Plan-Neofluar

M27

420351-9910-000	20x	0.50	Air	Plan Neofluar	2.0	Not Available	BF, PhC, Fluo	0.17
4	40x/0.75 Air	Zeiss	40x/0.75 Ph2 EC Plan-Neofluar

M27

	420361-9910-000	40x	0.75	Air	Plan Neofluar	0.71	Not Available	BF, PhC, Fluo	0.17
5	63x/0.75 Air	Zeiss	63x/0.75 Corr Ph2 LD Plan-Neofluar

M27

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

M27

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 5.5Zeiss AxioCam MRm
Expand
title Complete specifications
Camera

Zeiss AxioCam MRm

PCO Edge 5.5
Sensor Type

CCD

sCMOS
Sensor Category
Monochrome
Nb Pixels

1

5.

4

5 M
Pixel Layout

1388

2560 x

1040

2160
Pixel size
6.

45

5 um
Sensor size

8

16.

9

6 mm

x 6

x 14.

7

0 mm
Sensor diameter

11

21.8 mm
Bit depth

12

16-bit
Speed at full resolution

13

100 images/s
Max QE

55

60 % at 600 nm

Readout

Reading noise

8

1.0 e⁻
Cooling

Pelletier

Forced air +7C
Dark Current
0.

7

6 e⁻/pixel/sec
Full well capacity

17

30 000 e-
Dynamic Range
1:

2000

30000
Interface

FireWire (IEEE 1394a)

Dual Camera Link PCIe
Mount
C-mount

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Image Added
View file
name PCO_Edge 5.5_Datasheet.pdf
height 250
Zeiss Axiocam MRm (not installed)

Expand

title	Complete specifications

sCMOS55 2560 21605 16 mm x 140 21.8 16100

CameraPCO Edge 5.5	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	60 55 % at 600 nm
Reading Readout noise	1.0 8 e⁻
Cooling	Forced air +7CPelletier
Dark Current	0.6 7 e⁻/pixel/sec
Full well capacity	30 17 000 e-
Dynamic Range	1:300002000
Interface Dual Camera Link PCIe	FireWire (IEEE 1394a)
Mount	C-mount

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View file

name	Zeiss_AxioCam MRm_Datasheet.pdf
height	250

Tabs Page

id	User Guide
id	User Guide
title	User Guide

User Guide

UI Expand

expanded	true
title	Startup

If not already done, turn on the the computer (#1) and use your UdeM credentials to 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 bar (#3) on the desk near the computer
When using the instrument for the first time, it is necessary to import the microscope -specific parameters BEFORE configuration before starting the software. See the the First Use section below.
Start Zen

Running this procedure will

delete

erase all your experiment protocols and

restore

reset the software to its original settings (ask for support if you are not sure).

If Zen is open, close

Zen

it and wait

for

until it

to close

has completely shut down (this may take up to 30 seconds)
On the Desktop, open the Softwares

folder

folder
Double-click Zen Settings for

Axio-Osberver

Zeiss Z1-Colibri
A script will run and a black window will appear briefly

Click

OK

to close the message

When the message Settings for Zen have been imported successfully

.

appears, click OK to close it
You can

then

now open

Zen

Zen

UI Expand

title	First Use

Please note,

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

Note

UI Expand

title	Loading samples

During this procedure, you will:

Set

This procedure puts

the microscope

in

to a safe configuration

and performs

Perform a calibration
Load your sample
Find and adjust the focus

Once completed, your sample .At the end of this procedure the microscope will be ready for acquisition.

title

On the microscope touch screen:

If not already done,

press Home>Microscope>Control>Objectives>

select the lowest-magnification objective. On the microscope touch screen Home > Microscope > Control > Objectives > 2.5x

to select a safe objective

In Zen

:Once Zen software is

, once it has started a

popup

calibration dialog should

show up, just

appear. Simply click Calibrate Now.
The microscope will lower the objectives, perform

a

an XY calibration

and then

first, followed by a Z calibration, and then return to its original position.

UI Expand

title	Calibration

This step is required to calibrate the microscope in XY and Z. Doing a Performing this calibration will save you a lot of time to find your significantly reduce the time needed to locate and focus on your sample.

UI Expand

Calibration within the Zen Software

Tip

Once calibrated, the focus

can be

is typically found at Z = 1.1 mm for a microscope slide

). The Z value can be found

. 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

under Home > Z-Position

If the calibration popup dialog did not show up you at Zen opening, you can do it manually:

Select the Stage window (, as well as in Zen within the Focus tab, located on the right of Zen window) and click Calibrate

A warning message will show up click Continue

The microscope will lower the objectives perform a XY calibration

Then in the Focus Window on the right of Zen window) and click Calibrate

A warning message will show up click Continue

The microscope will lower the objectives perform a Z calibration

Done.

nce calibrated, the focus can be found at Z = 1.1 mm for a microscope slide). The Z value can be found on the microscope touch screen Home>Z-Position

UI Expand

title	Calibration with the touch screen

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.

On the microscope touch screen:

If not already done, Press Home>Load Position to lower the objectives to the lowest position

Press

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,

move

slightly adjust the focus

slightly up

upward to

remove

clear the Lower Z

limit reached

Limit Reached message displayed on the

touchscreen

If not already done, press Home>Microscope>Control>Objectives>5x to select the 5x 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 calibration procedure

Wait a few seconds for the calibration to be completed

Press Home>Microscope>XYZ>Position>XY-Position>Set zero>Auto to perform a stage calibration

Press OK to start the calibration procedure

Wait a few seconds for the calibration to be completed

Note
Once calibrated, the focus can be found at Z = 1.7 mm). The Z value can be found on the microscope touch screen Home>Z-Position

UI Expand

title	First focus

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

Warning

title	Important

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

On the microscope touch screen:

If not already done, press Home>Microscope>Turret>Objectives>5x to select the 5x objective

Info

The 5x objective is the safest because it has the longest working distance (12mm). 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 parafocal, focusing with the safest objective will then allow you to easily find your sample with another objective. The 10x objective is also safe because its working distance is 6.5 mm.

If not done already, press Home>Load Position to lower the objective to the lowest position and 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
Note
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 Zen

In the Locate tab, select BF or the desired fluorescence (DAPI, GFP, mPlum) to activate the configuration

Adjust the focus with the main dial while looking through the eyepieces until the image is perfectly sharp

Note
Once calibrated, the focus can be found at Z = 1.7 mm). 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

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
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
Navigate to Home > Microscope > XYZ > Position > XY-Position > Set Zero > Auto to perform a stage calibration
Press OK to start the calibration procedure
Wait a few seconds for 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	Initial focus

Warning

title	Important

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:

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

Info

The 2.5× and 10× objectives are the safest to use due to their long working distance (>6 mm). The sample will appear in sharp focus well before the objective approaches it. It is recommended to always focus using the safest objectives first. Since the objectives are parafocal, focusing with the safest objectives will facilitate locating the sample when switching to higher-magnification objectives.

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
Place the test slide on the microscope stage with the coverslip facing the objective
Note
title Important
Using a test slide will significantly reduce the time required to set up the instrument.
If necessary, adjust the stage to ensure that the sample is centred under the objective

In Zen:

In the Locate tab, select BF or the desired fluorescence (Fluo, DAPI, GFP, Cy3, Cy5) to activate the configuration
Adjust the focus with the main dial while looking through the eyepieces until the image is perfectly sharp

Info
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.

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

UI Expand

title	Seconday focus

Warning

title	Important

Perform the initial focus using the safest objective before switching to higher-magnification objectives.

UI Expand

title	Focusing with air objectives

After performing the initial

UI Expand

title	Seconday focus

Warning

title	Important

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

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

Press Home>Microscope>Control>Objectives, press 10x, 20x or 40x to select the desired objective

UI Expand

title	Focusing with air objectives

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) but has a smaller field of view. The 20x/0.8 objective offers the best compromise between Resolution and Field of View

Note
There are two (2) 40x objectives, make sure you select the Air 40x

In Zen :

In the Locate tab, select BF or the desired fluorescence (DAPI, GFP, mPlum) 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!

UI Expand

title	Focusing with oil objectives

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

Press

Home>Microscope>Turret>

Home>Microscope>Control>Objectives
Press

63x Oil

10x, 20x,

40x Oil

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

.

The microscope will automatically lower the stage so that the sample is accessible.

Info
The 40x

and 63x oil objectives provide the same spatial resolution because they have the same numerical aperture (1.4).
The 40x oil objective offers a larger field of view and transmits light slightly better beyond 700nm.
The 63x oil objective transmits light slightly better in the visible spectrum (440-710 nm) and has a better Strehl ratio (90%). It is particularly suited for super-resolution imaging, but its field of view is smaller.

objective is the best Air objective because it has the 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
Adjust the

Note
There are two (2) 40x objectives, make sure you select the 40x Oil

Place a single drop of oil on the objective

Press Done. The microscope will automatically return the objective to its original position

In Zen :

In the Locate tab, select BF or the desired fluorescence (DAPI, GFP, mPlum) to activate the configuration

Adjust the

focus with the precision dial while looking through the eyepieces

until the

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!

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

UI Expand

title

Loading samples

Focusing with oil objectives

After performing the initial focus, on the microscope

touch screen:

Press

Home>Load Position to lower the objectives 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>Control>Objectives>2.5x to select the 2.5x 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

Note
Once calibrated, the focus can be found at Z = 1.1 mm). The Z value can be found on the microscope touch screen Home>Z-Position

UI Expand

title	First focus

Warning

title	Important

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

On the microscope touch screen:

Press Home>Microscope>Turret>Objectives

Press 2.5x to select the 2.5x lens

Info
The 2.5x objective is the safest because it has the longest working distance (9 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 objectives 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
Note
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 Zen

In the Locate tab, select BF or the desired fluorescence (DAPI, GFP, Rhodamine, etc…) to activate the configuration

Adjust the focus with the main dial while looking through the eyepieces until the image is perfectly sharp

Note
Once calibrated, the focus can be found at Z = 1.1mm). 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	Secondary focus

Warning

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>Control>Objectives

Press 20x or 40x or 63x to select the desired lens

Info
The 40x objective is the best Air objective because it has the largest numerical aperture (0.75).

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

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

Press Home>Microscope>Control>Objectives
Press 63x Oil. The microscope will automatically lower the objective so that the sample is accessible
Place a drop of oil on your sample
Press Done. The microscope will automatically return the sample to its original position

In Zen:

In the Locate tab, select BF or the desired fluorescence (DAPI, GFP, Rhodamine, 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!

UI Expand

title	Storage management

Files can be 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 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, turn off the incubation module power strip (#2A) and close the CO₂ cylinder (#2B)
Select the 2.5x 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

Note

title	Important Reminders

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

Tabs Page

id	Lightpath
title	Lightpath

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

View file

name	Zeiss_Z1-Colibri_LightPath.pdf
height	250

Tabs Page

id	Manuals
title	Manuals

Available manuals

Tabs Page

id	Log
title	Log

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

Home>Microscope>Turret>Objectives
Press 63x Oil (1.4)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 the objective
Press Done. The microscope will automatically return the objective to its original position

In Zen :

In the Locate tab, select BF or the desired fluorescence (Fluo, DAPI, GFP, Cy3, DsRed, Cy5) 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 off the illumination

Your sample is ready for acquisition!

UI Expand

title	Storage management

Files can be 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 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 (#2A) and close the CO₂ cylinder (#2B)
Turn off the microscope power bar (#3)
Turn off the computer
Cover the instrument with the protective dust cover

Note

title	Reminder

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

Tabs Page

title	Log

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

UI Expand

title	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

title	Technical Datasheet

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

Condenser

Manual 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/0.075 Air 420320-9901-000
10x/0.25 Air Ph1 420941-9911-000
20x/0.5 Air Ph2 420351-9910-000
40x/0.75 Air Ph2 420361-9910-000
63x/0.75 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
- 24 GB DDR3 800 MHz (3 x 8 GB)
OS Drive
- 1 TB SSD 550 MB/s
- Win 11 23H2
Storage
- 2 TB HD 110 MB/s
Video 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 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

Consumables

CO₂ Tank
Oil
Lens Cleaner

Manuals

Tabs Page

title	Troubleshooting & FAQ

Troubleshooting

UI Expand

title	I don't see any fluorescence!

Technical support is free and unlimited. Contact us !

UI Expand

title	I see a high background in fluorescence

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

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.

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
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/0.075 Air 420320-9901-000
10x/0.25 Air Ph1 420941-9911-000
20x/0.5 Air Ph2 420351-9910-000
40x/0.75 Air Ph2 420361-9910-000
63x/0.75 Air Ph2 Long Distance 421381-9970-000
63x/1.4 Oil 420782-9900-000

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 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 MR R3 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 LG Flatron E2711 27' 1920 x 1080
Software Zen Blue 3.5 SN=1121159628-524292 HASP=1798977001

Incubation

Pecon stage top incubation

Consumables

CO₂ Tank
N₂ Tank
Oil
Lens Cleaner

Tabs Page

id	FAQ
title	Troubleshooting & FAQ

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:

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

FAQ

UI Expand

title	Can I use this microscope to look at cell in a dishperform timelapse experiments?

Yes, but... 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,

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	Can I use this microscope to perform timelapse experiments?	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

Image AddedImage AddedImage Added

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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	Plateformes:_Plat-foot-en

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Technical Datasheet

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Stage

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Incubation

Anti-vibration table

Consumables

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FAQ

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Light sources

Condenser

Objectives

Stage

Filters

Detector

Workstation

Incubation

Consumables

Troubleshooting