Zeiss Axioscan

Z1

7 Slide scanner

Desmarais Building, Room 5308-2
Simple Microscope usage price
This Instrument was kindly provided to the CI²B

by –

in 2025

Slide scanner

Transmitted light

Applications

Upright microscope
Widefield imaging

- Brightfield color and monochrome
- Fluorescence 5 channels
- Pseudo-Phase contrast

Fluorescence for dyes like DAPI, FITC, DsRed, Cy5 and Cy7

High-throughput imaging
Slide scanner

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Description

Light sources

LED lamp for transmitted light
Viluma 7 FR-R[G/Y]BV-UV for fluorescence

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title	Complete specifications

Channel	Emission peak (nm)	Compatible Dyes
UV	385/30	DAPI, Hoechst 33342, Hoechst 33258, Alexa Fluor 350, Alexa Fluor 405, Indo-1, eBFP / BFP, eGFP (wt), True Blue
V	423/44	Pacific Blue, Lucifer Yellow, Alexa Fluor 433, eCFP, Cerulean
B	469/38	FM1-43, Cy2, eGFP, NBD, MitoTracker Green, Alexa Fluor 488, Fluo-4, BCECF, Calcein, DiO SNAFL, YO-Pro-1, Nissl, LysoSensor Green, mHoneydew, FITC / Fluorescein, Kaede (green / red), PerCP, YoYo-1, FuraRed
G	555/30	TRITC, 7-AAD, Cy3, tdTomato, Alexa Fluor 546, Alexa Fluor 555, DsRed, mOrange, TagRFP, SNARF, DyLight 549, Spectrum Orange
Y	591/27	MitoTracker RED FM/CMXRos, txRed, mCherry, mRFP1, Cy3.5, Rhodamine B, Alexa Fluor 568, Dylight 594, Alexa Fluor 594, Bodipy TR
R	631/33	Alexa Fluor 633, Alexa Fluor 647, Cy5, DRAQ5, ToTo-3, ATTO-655, MitoTracker DeepRed, APC, ATTO-647N
FR	735/40	Alexa Fluor 750, Alexa Fluor 790, Cy7, Cy7.5

Total output 1510 mW

The information above does not directly indicate the effective intensity provided by the instrument as Zeiss does not provide the nominal power of their light sources,excepted the total output being 1510 mW. The graph on the left only indicates the emission filter bandwidth while the graph on the right compared the normalized relative intensities between the Viluma and the historic HXP 120 mercury bulb lightsource. Finally both graphs are misleading since they present 8 individual channels which can't be provided within the same product. The Viluma 7 can only provide 7 individual channel. In this case, the model included in this instrument does not have the Cyan Channel.
Zeiss_Viluma_Product Info.pdf

Objectives

5x/0.25 Air
10x/0.45 Air
20x/0.8 Air
40x/0.95 Air

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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	5x/0.25 Air	Zeiss	5x/0.25 Fluar	420130-9900-000	5x	0.25	Air	Fluar	12.5	>90% [410-800]	BF, Fluo	0.17
2	10x/0.45 Air	Zeiss	10x/0.45 Plan Apochromat	420640-9900-000	10x	0.45	Air	Plan Apocrhomat	2.0	>80% [380-900]	BF, Fluo	0.17
3	20x/0.8 Air	Zeiss	20x/0.80 Plan Apochromat	420650-9903-000	20x	0.80	Air	Plan Apochromat	0.55	>90% [400-800]	BF, Fluo	0.17
4	40x/0.95 Air	Zeiss	40x/0.95 Plan Apochromat	420660-9970-000	40x	0.95	Air	Plan Apochromat	0.25	>90% [480-780]	BF, Fluo	0.13 - 0.21
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Dichroic

Filter Set 112 LED SBP 405/495/575/654/761

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title	Complete specifications

Position	Name	Brand	ID	Excitation filter	Dichroic mirror	Emission filter
1	Filter Set 112 LED SBP	Zeiss	489112-9120-000	-	405/495/575/654/761	-
2	-
3	-
4	-
5	-
6	-

Emission filters

Empty-
DAPI
FITC
DsRed
Cy5
Cy7

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title	Complete specifications

Position	Name	Brand	ID	Excitation filter	Dichroic mirror	Emission filter	Comments
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2	DAPI	Zeiss	425/30 [412-438
3	FITC	Zeiss	514/30 [501-527
4	DsRed	Zeiss	592/25 [583-601
5	Cy5	Zeiss	[681/45
6	Cy7	Zeiss	[788/38

List of compatible dyes

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title	List of compatible dyesClick to Expand

Compatible Dyes	Excitation	Emission
1,8-ANS (1-Anilinonaphthalene-8-sulfonic acid)	375 nm	480 nm
1-Anilinonaphthalene-8-sulfonic acid (1,8-ANS)	375 nm	479 nm
5-FAM pH 9.0	492 nm	518 nm
5-ROX (5-Carboxy-X-rhodamine, triethylammonium salt)	578 nm	604 nm
5-ROX pH 7.0	578 nm	604 nm
5-TAMRA	549 nm	577 nm
5-TAMRA pH 7.0	553 nm	576 nm
5-TAMRA-MeOH	543 nm	567 nm
6,8-Difluoro-7-hydroxy-4-methylcoumarin pH 9.0	358 nm	450 nm
7-Hydroxy-4-methylcoumarin	360 nm	447 nm
7-Hydroxy-4-methylcoumarin pH 9.0	361 nm	448 nm
Alexa 405	401 nm	421 nm
Alexa 430	431 nm	540 nm
Alexa 488	493 nm	520 nm
Alexa 546	562 nm	573 nm
Alexa 555	553 nm	568 nm
Alexa 568	576 nm	603 nm
Alexa 633	632 nm	648 nm
Alexa 647	653 nm	669 nm
Alexa 660	664 nm	691 nm
Alexa 750	752 nm	780 nm
Alexa Fluor 430 antibody conjugate pH 7.2	431 nm	540 nm
Alexa Fluor 488 hydrazide-water	493 nm	518 nm
Alexa Fluor 555 antibody conjugate pH 7.2	553 nm	568 nm
Alexa Fluor 568 antibody conjugate pH 7.2	579 nm	603 nm
Alexa Fluor 633 antibody conjugate pH 7.2	631 nm	648 nm
Alexa Fluor 647 antibody conjugate pH 7.2	653 nm	668 nm
Alexa Fluor 647 R-phycoerythrin streptavidin pH 7.2	569 nm	666 nm
Alexa Fluor 660 antibody conjugate pH 7.2	663 nm	691 nm
Alexa Fluor 750 antibody conjugate pH 7.2	753 nm	779 nm
Allophycocyanin pH 7.5	651 nm	660 nm
APC (allophycocyanin)	650 nm	660 nm
Atto 647	644 nm	670 nm
Auramine O	431 nm	501 nm
BCECF pH 5.5	485 nm	521 nm
BFP (Blue Fluorescent Protein)	380 nm	439 nm
BO-PRO-1-DNA	462 nm	482 nm
BO-PRO-3-DNA	574 nm	604 nm
BOBO-1-DNA	461 nm	484 nm
BOBO-3-DNA	570 nm	605 nm
BODIPY 650/665-X, MeOH	646 nm	664 nm
BODIPY TMR-X antibody conjugate pH 7.2	544 nm	573 nm
Bodipy TMR-X conjugate	544 nm	573 nm
BODIPY TMR-X, MeOH	544 nm	570 nm
BODIPY TMR-X, SE	544 nm	570 nm
BOPRO-1	462 nm	482 nm
BOPRO-3	574 nm	604 nm
Calcein	493 nm	514 nm
Calcein pH 9.0	494 nm	514 nm
Calcium Orange	549 nm	574 nm
Calcium Orange Ca2+	549 nm	573 nm
Carboxynaphthofluorescein pH 10.0	600 nm	674 nm
Cascade Blue	398 nm	420 nm
Cascade Blue BSA pH 7.0	401 nm	419 nm
Cascade Yellow	399 nm	549 nm
Cascade Yellow antibody conjugate pH 8.0	399 nm	549 nm
CFDA	495 nm	517 nm
CFP (Cyan Fluorescent Protein)	434 nm	474 nm
CI-NERF pH 2.5	504 nm	541 nm
Coumarin	360 nm	447 nm
Cy 2	489 nm	503 nm
Cy 3	549 nm	562 nm
Cy 3.5	578 nm	591 nm
Cy 5	646 nm	664 nm
Cy 7	751 nm	778 nm
DAPI	358 nm	463 nm
DAPI-DNA	359 nm	461 nm
Dapoxyl (2-aminoethyl) sulfonamide	372 nm	582 nm
DDAO pH 9.0	648 nm	657 nm
Di-8 ANEPPS	469 nm	630 nm
Di-8-ANEPPS-lipid	469 nm	631 nm
DiI	551 nm	565 nm
DiO	487 nm	501 nm
DiR	750 nm	779 nm
DiR-lipid	750 nm	779 nm
DM-NERF pH 4.0	493 nm	530 nm
DsRed	563 nm	581 nm
DTAF	495 nm	517 nm
dTomato	554 nm	581 nm
DyLight 405	399 nm	434 nm
DyLight 488	493 nm	518 nm
DyLight 549	555 nm	569 nm
DyLight 633	624 nm	646 nm
DyLight 649	652 nm	668 nm
DyLight 750	751 nm	772 nm
DyLight 800	771 nm	796 nm
eCFP (Enhanced Cyan Fluorescent Protein)	437 nm	476 nm
eGFP (Enhanced Green Fluorescent Protein)	488 nm	509 nm
Ethidium Bromide	524 nm	605 nm
Ethidium homodimer	528 nm	617 nm
Ethidium homodimer-1-DNA	528 nm	617 nm
evoglow-Bs1	448 nm	496 nm
evoglow-Bs2	448 nm	496 nm
evoglow-Pp1	448 nm	495 nm
FDA	495 nm	517 nm
FITC	495 nm	517 nm
FITC antibody conjugate pH 8.0	495 nm	519 nm
Fluo-4	494 nm	516 nm
Fluor-Ruby	554 nm	582 nm
Fluorescein	495 nm	517 nm
Fluorescein 0.1 M NaOH	493 nm	513 nm
Fluorescein antibody conjugate pH 8.0	493 nm	517 nm
Fluorescein pH 9.0	490 nm	514 nm
Fluoro-Emerald	495 nm	524 nm
FM 1-43	472 nm	578 nm
FM 1-43 lipid	473 nm	579 nm
FM 4-64	508 nm	751 nm
FM 4-64, 2% CHAPS	506 nm	751 nm
Fura Red Ca2+	435 nm	670 nm
Fura Red, high Ca	434 nm	659 nm
Fura Red, low Ca	472 nm	673 nm
Fura-2, no Ca	367 nm	515 nm
GFP (S65T)	489 nm	509 nm
Lissamine rhodamine	572 nm	590 nm
LOLO-1-DNA	568 nm	580 nm
Lucifer Yellow, CH	428 nm	542 nm
LysoSensor Blue	374 nm	424 nm
LysoSensor Blue pH 5.0	374 nm	424 nm
LysoSensor Green	447 nm	504 nm
LysoSensor Green pH 5.0	447 nm	502 nm
LysoSensor Yellow pH 3.0	389 nm	542 nm
LysoTracker Blue	373 nm	421 nm
Magnesium Orange	550 nm	575 nm
Marina Blue	362 nm	464 nm
mCherry	587 nm	610 nm
mHoneydew	478 nm	562 nm
MitoTracker Green	490 nm	512 nm
MitoTracker Green FM, MeOH	490 nm	512 nm
MitoTracker Orange	551 nm	575 nm
MitoTracker Orange, MeOH	551 nm	575 nm
mOrange	548 nm	562 nm
mPlum	587 nm	649 nm
mRFP	585 nm	608 nm
mStrawberry	575 nm	596 nm
mTangerine	568 nm	585 nm
NBD-X	466 nm	534 nm
NBD-X, MeOH	467 nm	538 nm
NeuroTrace 500/525, green fluorescent Nissl stain-RNA	497 nm	524 nm
Nile Blue, EtOH	631 nm	660 nm
Nile Red	559 nm	637 nm
Nile Red-lipid	553 nm	636 nm
Nissl	497 nm	524 nm
Phycoerythrin	565 nm	575 nm
PO-PRO-3	539 nm	571 nm
PO-PRO-3-DNA	539 nm	571 nm
POPO-3	533 nm	573 nm
Propidium Iodide	538 nm	617 nm
Propidium Iodide-DNA	538 nm	619 nm
Quasar 570	549 nm	562 nm
R-Phycoerythrin pH 7.5	565 nm	576 nm
Resorufin	571 nm	584 nm
Resorufin pH 9.0	571 nm	584 nm
Rhod-2	552 nm	577 nm
Rhod-2 Ca2+	553 nm	578 nm
Rhodamine	551 nm	573 nm
Rhodamine 110 pH 7.0	497 nm	520 nm
Rhodamine B	543 nm	565 nm
Rhodamine phalloidin pH 7.0	558 nm	575 nm
Rhodamine Red-X antibody conjugate pH 8.0	573 nm	591 nm
Rhodaminen Green pH 7.0	497 nm	523 nm
Rhodol Green antibody conjugate pH 8.0	499 nm	524 nm
Sapphire	396 nm	511 nm
SYBR Green I	498 nm	522 nm
SYPRO Ruby	467 nm	618 nm
SYTO 13-DNA	488 nm	506 nm
SYTO 17-DNA	619 nm	638 nm
SYTO 45-DNA	451 nm	486 nm
SYTOX Blue-DNA	445 nm	470 nm
Tetramethylrhodamine antibody conjugate pH 8.0	552 nm	578 nm
Tetramethylrhodamine dextran pH 7.0	555 nm	582 nm
TO-PRO-3-DNA	642 nm	657 nm
TOTO-3-DNA	642 nm	661 nm
TRITC	550 nm	573 nm
YO-PRO-1-DNA	491 nm	507 nm
YOYO-1-DNA	491 nm	509 nm

Detectors

Zeiss AxioCam 705 Color

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title	Complete specifications

Camera	Zeiss AxioCam 705 Color
Sensor Type	CMOS
Sensor Category	Color
Nb Pixels	5.07 M
Pixel Layout	2464 × 2056
Pixel size	3.45 µm × 3.45 µm
Sensor size	8.5 mm x 7.1 mm
Sensor diameter	11.1 mm
Bit depth	14-bit
Speed at full resolution	60 images/s
Max QE	80 % @ 540nm
Readout noise	2.2 e⁻
Cooling	18C Thermoelectric
Dark Current	0.5 e⁻/pixel/sec
Full well capacity	11 000 e-
Dynamic Range	1:5000 1: 25 000 HDR mode
Interface	USB B 3.0
Mount	C-mount

Zeiss_Axiocam_705-color_Product info.pdf

Hamamatsu ORCA-Flash4.0 V3

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title	Complete specifications

Camera	Hamamatsu ORCA-Flash4.0 V3
Sensor Type	sCMOS
Sensor Category	Monochrome
Nb Pixels	4.2 M
Pixel Layout	2048 x 2048
Pixel size	6.5 um
Sensor size	13.312 mm x 13.312 mm
Sensor diameter	18.826 mm
Bit depth	16-bit
Speed at full resolution	30 images/s
Max QE	82 % at 560 nm
Reading noise	0.8 e⁻
Cooling	Air cooled -10C
Dark Current	0.06 e⁻/pixel/sec
Full well capacity	30 000 e-
Dynamic Range	1:37000
Interface	USB 3.0 or Camera-Link
Mount	C-mount

User Guide

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title	Startup

User Guide

Tip
This instrument is only offered with service. Please contact us.

If not already done, turn on the computer (#1) and log in to Windows using your UdeM credentials
Turn on the instrument power bar (#2) on the desk between the instrument and the computer
Turn on the instrument (#3) on the left side of the instrument
Start Zen

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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.

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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
Turn off the microscope power bar (#1)
Turn off the computer

Reminder

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

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Log

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title	2025-09-12 Added to the wiki

Added to the Wiki

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title	2025-05-01 Direct connection to Processing workstation

Connected to Processing workstation with 10 GB cable

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title	2025-02-01

Purchase and Installation

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title	Technical Datasheet

Technical Datasheet