Zeiss Apotome

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General information

  Zeiss inverted microscope with automatic XY stage, motorized focus, large field sCOMS camera, autofocusing, background rejection imaging and live experiment support.

Application
  • Brightfield and multi-channel fluorescence imaging of fixed/live samples
  • 2-channel simultaneous fluorescence imaging
  • Option of Apotome insert to remove fluorescence background
  • Isis imaging platform for color karyotyping, comparative genomic hybridization (CGH), mFISH, multicolor fluorochrome banding (mBAND), and telomere measurement
  • Optimized to live experiments
Accessibility
Microscope details
  • Microscope frame: Zeiss Observer Z1
  • Objectives: 5x/0.15, 10x/0.25, 40x/1.3 Oil DIC, 63x/1.4 Oil, 100x/1.4 Oil DIC
  • Fluorescence light source: Zeiss Colibri 7 LED
  • Brightfield imaging mode: BF, DIC and Phase Contrast (Ph1 only)
  • Dual camera splitter: Cairn Research TwinCam
  • Camera
    • Transmission arm: Flash4.0 Lite (sCMOS: 2048x2048, 6.45um, 16 bits, 30 fr/s)
    • Reflection arm: Flash4.0 Lite (sCMOS: 2048x2048, 6.45um, 16 bits, 30 fr/s)
  • XY Stage: Zeiss stepper motor stage
  • Z focus: motorized objective focus
  • Auto-focusing: Zeiss Definite Focus 2 (hardware) and software
  • Zeiss Apotome.2 insert: optical sectioning using structured illumination
  • Isis imaging platform: Metasystems
  • Isis camera: MetaSystems CoolCube 1m (monoCCD:1360x1024, 6.45 μm, 12 bits, 15fr/s)
  • Live experiment support: heated live chamber (37 deg.) and 5% CO2 (humidified)
  • Sample holder: options of slide, dish and well plates
  • Optical bench: passive
  • Commercial dervice contract: Zeiss Protect Premium (microscope, stage and computer), -June 2020
Filter settings
Default setup
Fluorophores DAPI GFP Cy3 Cy5 BF, Ph1 DIC
LED 385/30 (UV) 469/38 (B) 555/30 (G) 631/33 (R) White LED
Filter cube 90 HE LED, BS:405/493/575/653, Em:425/30+514/30+592/25+709/100(Pos1 default)
Alternative filter cube 90 HE LED (Pos1) BP470/40-FT495-BP525/50 (Pos2) BP550/25-FT570-BP605/70 (Pos3) BP640/30-FT660-BP690/50 (Pos4) Empty Analyser

Alternative setup
Fluorophores CFP YFP HcRed
LED 423/44 (V) 511/44 (C) 590/27 (Y)
Filter cube 91 HE LED, BS:450/538/610, Em:467/24+555/25+687/145 (backup)

Dual camera setup
Typical fluorophores DAPI,CFP, GFP, YFP Cy3, HcRed, Cy5
Camera arms Transmission (T) Reflection (R)
Beamsplitter 565 nm SP
Emission filter fluoeophore dependant fluoeophore dependant

Condenser setup
Contrast Phase contrast BF DIC
Component Ph1 ring (Pos1) Empty (Pos2) IX2-DIC20 (Pos3) IX2-DIC40 (Pos4) IX2-DIC60 (Pos5)
Matched Objective 10x ph1 and 20x ph1 Any 10x, 20x 40x 60x and 100x

Workstation and software
  • Acquisition software: Zeiss Zen (blue)
  • Isis acquisition software: Isis
  • Acquisition workstation
    • CPU: Intel Xeon E5-2620
    • OS: Windows 10
    • RAM: 16 GB
    • Local data drive: 1 TB
    • Network name:
Images taken from Apotome
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