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url	Zeiss Z1 Colibri

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id	Instrument Tabs
direction	horizontal

Tabs Page

id	Description
title	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

Zeiss Colibri 7

Objectives

Image Added

Objectives

2.5x/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

Zeiss AxioCam MRm

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

Zeiss_AxioCam MRm_Datasheet.pdf

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

PCO_Edge 5.5_Datasheet.pdf

Tabs Page

id	User Guide
title	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 tank near the sink
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 starting configuration into the software. See 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

Observer 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

This procedure puts During this procedure, you will set the microscope in to a safe configuration and performs , perform a calibration.At the end of this procedure the microscope , load your sample, and adjust the focus. Once completed, your sample will be ready for acquisition.

If not already done, select the lowest-magnification objective.

On the

microscope touch screen

:If not already done, press Home>Microscope>Control>Objectives>

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 click

appear

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

title	Calibration within the Zen Software

Info

Once calibrated, the focus is typically

Once calibrated, the focus can be

found at Z = 1.1 mm for a microscope slide

)

.
The Z

value

position can be

found

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

side of the screen.

Calibration with the touch 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. To verify whether the system is calibrated, simply…

UI Expand

title	Manual calibration with the software

O

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

Select the Stage window (on the right of Zen window) and click Calibrate

A

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

XY calibration

Done.

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

nce calibrated, the focus can

be found at Z =

1.1 mm

1.1 mm for a microscope slide). The Z value can be found on the microscope touch screen Home>Z-Position

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	Manual calibration on 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.
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
Calibration is now complete

for a microscope slide). The Z value can be found on the microscope touch screen Home>Z-Position

UI Expand

title

Make sure the calibration dialog is displayed at startup

On the microscope touch screen:

If not already done, Press Home>Load Position to lower the objectives to the 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
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	Calibration with the Software

I

If

UI Expand

title	First focus

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

UI Expand

title	Seconday focus

Warning

title	Important

First focus with the safest objective 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 10x, 20x or 40x to select the desired 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) 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>Objectives

Press 63x Oil, 40x Oil 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.

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 image is perfectly sharp
In the Locate tab, select Off to turn the illumination off
Your sample is ready for acquisition!

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 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

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 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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Old Version 61

New Version 62

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Zeiss Axio-Observer Z1 Colibri inverted microscope

Light sources

Objectives

Objectives

Filter

Detectors

Stand

Light sources

Condenser

Objectives

Stage

Filters

Detector

Workstation

Incubation

Consumables

Troubleshooting

FAQ

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Versions Compared

Old Version 61

New Version 62

Key

Zeiss Axio-Observer Z1 Colibri inverted microscope

Light sources

Objectives

Objectives

Filter

Detectors

Stand

Light sources

Condenser

Objectives

Stage

Filters

Detector

Workstation

Incubation

Consumables

Troubleshooting

FAQ