Advanced Light Microscopy and Image Analysis Facility (ALMIA)

Vínculos rápidos:
1. SERVICE DEFINITION
2. OFFERED SERVICES
3. PERSONNEL AND CONTACT
4. EQUIPMENT
5. RATES
6. PUBLICATIONS AND WEB RESOURCES
7. BIBLIOGRAPHY (UPO)

1. SERVICE DEFINITION

Researchers at the Andalusian Center for Developmental Biology (CABD) use light microscopy as a tool to study development of cells, organs and embryos in different model organisms. Most of the experimental systems under analysis display complex 3D organisation both at the cellular and organismal levels. Thus, access to the appropriate microscopic technique to unveil this complexity becomes of paramount importance.

The Advanced Light Microscopy and Image Analysis Facility (ALMIA) provides training and support to scientists in a wide-range of image acquisition and analysis techniques. Instruments in the unit range from wide-field imaging systems to in toto imaging systems for whole-embryo morphogenesis studies. The facility is specialised in the following areas of expertise:

   Advanced live-cell imaging using wide-field and spinning disk imaging systems
   High-quality confocal scanning light microscopy
   High and super-resolution microscopy
   Whole model organism imaging using light-sheet microscopy.

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2. OFFERED SERVICES

    A. Microscopy Techniques:

  • Wide-field
     
  • Confocal Microscopy
     
  • High and super-resolution microscopy
        PALM/STORM
        Zeiss Airyscan
        Leica LIGHTNING

  • In toto Imaging (Lightsheet)
     
  • Advanced microscopy
        Multiphoton microscopy
        Laser Ablation

    B. Image and Data Analysis

  • Consulting and design of experiments involving image analysis and microscopy
  • Analysis and interpretation of biological images
    • Tools: FIJI, Imaris
  • Statistical analysis of results obtained from image analysis
    • Tools: R, Orange3
  • Design and automatization of image analysis pipelines
    • Tools: Macro Scripting
  • Application of data mining and data science techniques to biological datasets involving images.
    • Tools: Python, Machine Learning, Clustering Techniques
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3. PERSONNEL AND CONTACT


Fernando Casares - Scientific Coordinator.
 
Katherina García - Head Technician. CSIC.  954977432.
 
Alejandro Campoy - Image data Analyst. 954978965.
 
Juan Carlos Millan - Technician.
 
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4. EQUIPMENT

The Advanced Light Microscopy and Image Analysis Facility at the CABD is equipped with the following instruments:

 

1. Confocal Microscope Leica SPE
  • Vertical Microscope DM 2500
  • Objetives: 10x air, 20x multi-immersion, 40x oil, 63x oil
  • Detectors: 1 PMT with spectral detection
  • Laser lines: 405 nm, 488nm, 532nm, 635nm
  • Software: LAS X

 

2. Restoration Microscopy System DeltaVision
  • Inverted Microscope Olympus IX71
  • Objetives: 10x air, 20x air, 40x oil, 60x oil, 100x oil
  • Camera: CoolSnap HQ
  • Temperature Control
  • Filter Configuration:

Excitation

Emission

360/40

457/50

436/10

465/30

470/40

528/38

492/18

535/30

555/28

617/73

640/20

685/40

  • Brightfield illumination and DIC
  • Software: Softworx

 

3. Fluorescence Microscope Zeiss Axio Imager. M2
  • Upright Microscope
  • Objectives: 10x air, 20x air, 40x air, 63x oil, 100x oil
  • Camera: AxioCam MRm
  • Filter Configuration:

Excitation

Emission

365

445/50

470/40

525/50

546/12

575-640

640/30

690/50

  • Apotome Module
  • Brightfield and DIC
  • Software: AxioVision

 

4. Confocal Microscope Nikon A1R
  • Inverted Microscope Nikon Eclipse Ti
  • Objectives: 10x air, 20 IMM, 40x oil, 60x oil
  • Laser Lines 405nm, Ar (457nm, 488nm, 514nm), 561nm, 640nm
  • 32-channel spectral detector 400 to 750 nm
  • 1 transmission detector
  • 4-channel detectors (PMT) with filters
  • Emission Filters: 450/50, 482/35, 525/50, 540/30, 515/30, 595/50, 585/50, 700/75
  • Temperature Control
  • CherryTemp for fast temperature shift during live cell imaging
  • Software: NIS-Elements

 

5. Spinning Disk Roper Scientific-Photometrics
  • Inverted Microscope Olympus IX-81
  • Yokogawa CSU-X1
  • Objectives: 10x air, 20x air, 40x air, 63x oil, 100x oil
  • Laser Lines: 405nm, 491nm, 561nm
  • Emission Filters: 460/50, 480/40, 525/50, 535/30, 630/75
  • Camera: CoolSnap HQ2 or Evolve
  • Brightfield and DIC
  • Temperature control
  • Objective Heater
  • FRAP, Photoablation (355nm) and TIRF
  • Software: Metamorph

 

6. Confocal Microscope Leica SP5 MP- AOBS
  • Inverted Microscope DMI 6000
  • Objetives: 10x air, 20x IMM, 25x water, 40x oil, 63x oil
  • Detectors: 2 PMT and 2 HyD with spectral detection
  • Galvo and Resonant Scanner
  • Laser lines: 405nm, Ar multiline, 561nm, 594nm, 633nm
  • Multiphoton Laser Mai Tai Deep See 690-1040nm
  • 2 external non-descanned detectors (NDDs) for Multiphoton Microscopy
  • Temperature Control
  • Software: LAS AF

 

7. Confocal Microscope Zeiss 880 Airyscan-Elyra
  • Inverted Microscope
  • Objectives: 10x air, 25x IMM, 40x water, 63x oil, 100x oil
  • Detectors: 2 PMT and 1 GaAsp with spectral detection
  • High Resolution: Airyscan
  • Laser Lines: 405, Ar multiline, 561, 633
  • Elyra Module: STORM/PALM. Laser lines 405nm, 488nm, 640nm
  • Temperature and CO2
  • Software: Zen

 

8. Confocal Microscope Leica Stellaris 5
  • Inverted Microscope DMI8
  • Objectives: 10x air, 20x air, 20x IMM, 40x air, 40x oil, 63x oil
  • Detectors: 4 HyD S with spectral detection
  • Laser Lines: 405nm, 488nm, 561nm, 638nm
  • High resolution: LIGTHNING
  • Software: LAS X

 

9. Spinning Disk 3i (Intellingent Imaging Innovations)
  • Zeiss Axio Observer 7 inverted microscope
  • Yokogawa CSU-W1
  • Objectives: 63x/1.4 oil, 100x/1.46 oil
  • Laser lines: 405nm, 445nm, 488nm, 514nm, 561nm, 640nm
  • Emission Filters: 445/45, 482/35, 525/30, 525/50, 542/27,617/73, 692/40
  • Camera: PRIME 95B
  • Brightfield and DIC
  • Temperature control
  • Software: Slide Book

 

10. Zeiss Lightsheet 7
  • Illumination Optics: 5x/0.1 and 10x/0.2, both with focus rings to adapt to refractive index (RI) of medium.
  • Detection optics:
    • 5x/0.1 and 10x/0.2, both with focus rings to adapt to refractive index (RI) of medium.
    • 20x/1.0 suitable for clearing methods with RI=1.53 +/- 0.05
  • Laser Lines: 405nm, 488nm, 561nm, 638nm
  • Dual camera for two colour simultaneous image acquisition
  • Incubation system: heating, cooling, CO2 chamber
  • Dedicated chambers and sample holders for small and large cleared specimens
  • Software: Zen

 

11. Workstation Zen

FIJI

ZEN

Imaris Viewer

12. Workstation Zeus

FIJI

IMARIS

13. Workstation Genesis

FIJI

IMARIS

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5. RATES

Services offered
RATES 2024 (without IVA)
UPO University and OPIs Company/Others
Confocal 5€/h 15€/h 20€/h
Widefield Delta Vision 3€/h 9€/h 12€/h
Widefield Axio Imager 2€/h 6€/h 8€/h
Lightsheet 5€/h 15€/h 20€/h
Image Analysis (1 hour of free advice) 15€/h 30€/h 60€/h
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6. PUBLICATIONS AND WEB RESOURCES

Fluorescence spectra viewer

https://www.thermofisher.com/order/fluorescence-spectraviewer#!/

https://www.bdbiosciences.com/en-us/resources/bd-spectrum-viewer

 

Fluorescent Protein Database

https://www.fpbase.org/

 

Microscopy Education

http://microscopy.fsu.edu/primer/index.html

www.microscopyu.com/

https://www.olympus-lifescience.com/en/microscope-resource/

 

Spanish Advanced Optical Microscopy Network

https://remoa.net/

 

Spanish Microscopy Society

https://microscopia.org/

 

European Light Microscopy Iniciative

https://elmi.embl.org/

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7. BIBLIOGRAPHY (UPO)

1. Fluorescence microscopy (1998) Herman, Brian
Oxford: BIOS Scientific Publishers, cop.
(535 HER flu)

2. Introduction to light microscopy (1998) Bradbury, Savile
Oxford (U.K.): Bios Scientific Publishers; New York: Springer
(577 IN)

3. Confocal microscopy: methods and protocols (1999)Totowa, N.J.
Humana Press, cop.
(57 CON)

4. Imaging Living Cells (1999) Rosario Rizzuto. Cristina Fasolato.
Berlin: Springer
(576 IMA)

5. In situ hybridization in light microscopy (2001) Gérard Boca Ratón
(Florida): CRC Press, cop. 2001
(577 MOR in)

6. Methods in cellular imaging (2001)
Oxford: Oxford University Press
(57 MET)

7. Cell biological applications of confocal microscopy (2002)
San Diego: Academic Press, cop.
(576 CELL)

8. Confocal Microscopy for Biologists (2004) Hibbs, A.R.
(57 HIB con)

9. Live cell imaging: a laboratory manual (2005)
Cold Spring Harbor (New York): Cold Spring Harbor Laboratory Press, cop.
(576 LIV)

10. Cell Imaging (2006) D. Stephens.
(576 CELL)

11. Handbook of Biological Confocal Microscopy (2006) Pawley, J. 
Plenum
(57HAN)
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CABD - Centro Andaluz de Biología del Desarrollo

Universidad Pablo de Olavide
Carretera de Utrera km1
41013 Sevilla, España
+34 954977911

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