UPSC has several microscopes where bright field, DIC, dark field, phase contrast and epifluorescence imaging can be performed.
Microscopes available at UPSC:
Epifluorescence microscope Leica DMi8
The microscope is inverted, fully motorized with a scanning stage
Microscope Leica DMi8 at UPSC. and motorized focus to allow Z stack acquisition. There are seven objective lenses 5x/0.15, 10x/0.32, 20x/0.4 corr 0-2 mm DIC, 40x/0.6 corr 0-2 mm DIC, 40x/1.1 water corr DIC, 63x/1.3 glycerol corr DIC and 100x/1.32 oil DIC. The change between objectives is made with parafocality, automatic adjustment for Koehler illumination and contrasting method allowing full reproducibility between sessions. In addition, fluorescence imaging for DAPI, GFP and mCherry can be made with fast switching between brightfield/DIC and fluorescence. There are also conventional filter sets for DAPI LP and BP filter, CFP, GFP LP and BP filter, YFP, RFP, and Cy5 (only visible by camera) where the 16 individually selectable LED light sources (in the range of 365-770 nm) can be fully controlled by the software. There are holders for slides of different length, 3 cm round Petri dishes and multiwell plates. The system is equipped with a Leica DFC 7000 T color camera which is sensitive enough for fluorescence and can do imaging at 40 fps. In addition, there is an even more sensitive monochrome Leica DFC 9000GT sCMOS camera with improved signal-to-noise ratio compared to the color camera. The system can be fully controlled by the software to allow easy changes between objectives, different fluorescence/DIC/bright field settings, stage positions, focus in combination with time lapse. The system is also triggered for fast imaging possibilities.
It has LAS X navigator for easy imaging options where one can do preview overview imaging of the whole sample. This overview can then be used to select one or more interesting regions for further imaging at high resolution where tile and stitching will be automatically recognized by the software when the sample is too large to fit in one image with the selected objective. There are autofocus algorithms or manual possibility to keep focus along a sample for tile imaging, which makes it possible to “straighten out” an unevenly mounted sample. In addition, the software can do 2D deconvolution of fluorescence images or extended depth of focus for color images.
Applications: Virtually any microscopy work that can be done on an inverted stage, which does not need phase contrast or dark field.
This microscope is located in room KB.K6 (B6.22.49) This instrument is operated on an hourly fee basis. You are allowed to use this microscope only after passing a mandatory introduction! A basic introduction to this instrument usually takes 2 h. Due to heavy usage, expect to wait 3 weeks or more for an introduction. For introduction or other questions regarding this instrument, please contact Marta Derba-Maceluch.
Epifluorescence microscope Zeiss Axioplan 2
Poplar stem section stained for lignin detection (Mule staining).
Axioplan 2 microscope at UPSC.
The microscope is upright, manual, equipped with colour CCD camera and a range of objectives (4x-100x). Microscope is equiped in conventional filter sets DAPI, GFP/YFP LP, RFP LP, GFP, CFP and CFP+GFP. MIcroscope is eqiped in Lumencor SOLA SM II Solid State White Light Engine LED lamp.
This microscope is located in room KB.K6 (B6.24.51) This instrument is operated on an hourly fee basis. You are allowed to use this microscope only after passing a mandatory introduction! For introduction or other questions regarding this instrument, please contact Marta Derba-Maceluch.
Epifluorescence microscope Zeiss AxioObserver A1m
Zeiss AxioObserver A1m at UPSC.
Fragment of poplar stem, cross section with visible tension wood. The microscope is inverted, manual, it has equipped with colour CCD camera and a range of objectives (4x-100x) with 2 of then as long working distans objective perfect for observation of bigger objects like callus. There are holders for slides of different length, 3 cm round Petri dishes and multiwell plates. Microscop is equipped with standard mercury bulb. This instrument is operated on an hourly fee basis. You are allowed to use this microscope only after passing a mandatory introduction! For introduction or other questions regarding this instrument, please contact Marta Derba-Maceluch.
Other available microscopes:
Zeiss AxioStar upright epifluorescence microscope equipped with standard mercury lamp and 10x-40x objectives is located in room KB.K6 (B6.20.51).
Zeiss Axioplan upright microscope equipped with colour CCD camera and computer is available to borrow from facility.
Axiovert 40 CFL inverted long working distance inverted epifluorescence microscope with holders for Petri dishes and multiwell plates equipped with standard mercury lamp and monochromatic CCD camera. located in room KB.K6 (B6.18.51).
Zeiss Standard 25 small upright microscope with two pair oculas for simuntaniosly observation by two persons. located in room KB.K6 (B6.18.51). 
Whole cross section of poplar stem from microscope, stained for starch.Stereomicroscopes available at UPSC:
Leica M205 FA stereomicroscope with Fluorescence
Fully motorized system with parafocal objectives of 0.63x Plan-Apo 
Epifluorescence strereomicroscope Leica M205FA at UPSC.with a working distance of 67 mm and 2x/0.35 Plan-Apo with a working distance of 20.1 mm and a 0-5 mm correction ring for water pillar (or agar). The objectives are mounted on a revolving nosepiece and can achieve 4.7 - 320x zoom magnification range that corresponds to a work field diameter of 46.1 – 0.72 mm.
It has episcopic light via gooseneck LED lamps and transmitted light via a light base that is equipped with motorized Rottermann contrast TM, brightfield and two-sided darkfield. Fluorescence by LED light source and bandpass filter sets for DAPI, CFP, GFP, YFP and RFP, in addition to long pass filter set for GFP. A DMC6200 digital pixel shift color camera is used for image acquisition. In addition, it is also equipped with a sensitive monochrome Leica DFC 9000GT sCMOS camera for improved fluorescence imaging. The stereomicroscope has ergonomic setup of ocular, tube and light base.
With this system one can do imaging of brightfield and/or fluorescence multichannel acquisition, time lapse images, 3D/Z stacks, overview images of large field of views, tile scan acquisition and stitching, spiral scan acquisition, 2D deconvolution and it has several analysis tools.
Applications: fast screening of fluorescence zygosity on plates with fast overview imaging or ocularly, GUS overview images and then more detailed imaging over large areas using tiles and stitching etc.
The stereomicroscope is located in the room inside KB.K6 (B6.22.49). This instrument is operated on an hourly fee basis. You are allowed to use this stereomicroscope only after passing a mandatory introduction! A basic introduction to this instrument usually takes 2 h. Due to heavy usage, expect to wait 3 weeks or more for an introduction. For introduction or other questions regarding this instrument, please contact Marta Derba-Maceluch or Judith Felten.
THUNDER Model Organism
This system is built on the Leica M205FCA stereomicroscope. This is the semi-motorized version with two objectives: 1x PlanApo, with a 61.5 mm working distance, equipped with the FluoCOMBI and 5x macro, with a 19 mm working distance, giving a shift in the light axis, making the M205FCA a macroscope (Parallax free imaging), also equipped with the FluoCOMBI. The maximum magnification of this microscope is 640x, with max NA of 0.5.
The system is equipped with a TL3000ergo transmitted light base, mounted with a high precision scanning stage that can be manually operated or motor controlled without losing linearity. The Rotterman contrast and darkfield are set manually and only from one side. However, the on/off switch and the intensity are both modulated through the software and the mirror tilt (Rotterman and darkfield) is coded in the software. It is thus possible to restore settings. The system is equipped with a sensitive monochrome Leica DFC 9000GT sCMOS camera, and fast CMOS Leica K5C color camera, the light source SOLA SM (with DAPI wavelength 365 nm) and the bandpass filter sets for DAPI, GFP, CFP, YFP and RFP (some additional filters are accessible on the LeicaM205FA).
Due to the macro configuration, the FluoCOMBI needs a separate dichroic in the light path that is matched to the standard filter used. We have two of such dichroics: 1) a quad dichroic which works for DAPI, GFP, RFP and Cy5; and 2) a multiband dichroic for CFP/YFP and mCherry.
Possible applications: high magnification, high resolution imaging. The system allows high-quality 3D images of thick samples, imaging of brightfield and/or fluorescence multichannel acquisition, time lapse images, 3D/Z stacks, overview images of large field of views, tile scan acquisition and stitching, spiral scan acquisition, 2D deconvolution and it has several analysis tools. , at the same time, benefits from the speed and sensitivity of a widefield system by using an optodigital method called Computational Clearing.
Example of Computational Clearing used on THUNDER microscope, left side fluorescent picture, right side after Computational Clearing.
The stereomicroscope is located in the room inside KB.K2 (B2.18.51). This instrument is operated on an hourly fee basis (please check price tab). You are allowed to use this stereomicroscope only after passing a mandatory introduction! A basic introduction to this instrument usually takes 2 h. For introduction or other questions regarding this instrument, please contact
Microscope THUNDER model organism at UPSC
Greenhouse equipment:.
Leica MZFL III epifluorescence stereomicroscope
This microscope allows fast screening of fluorescence (filter sets for CFP, GFP, YFP and RFP). Allows 8-100x magnification. This microscope is in the greenhouse dark room on floor 2.
Stereo fluorescence Microscope Leica AFL III at UPSC
Arabidopsis vascula boundle staind whit Toluidine blueCrossing stereomicroscope, Leica S9i
This stereomicroscope is suitable for 3D viewing with 12 mm depth of field and 37.7 mm object field. Zoom 6.3x-60x. Working distance 81 mm. This microscope possesses an inbuilt camera that is connected directly to a screen. An SD chip can be used to save images. This microscope is in the greenhouse on floor 2 at the photo station.
Microscope Leica S9i at UPSCScreening stereomicroscope Leica M125C
Zoom 10.8:1 with 1x plan apo objective (8x-100x); zoom information is coupled to the software to include scale as a parameter in the image. Working distance 61.5 mm. Equipped with stage TL3000Ergo with easy maneuver of transmitted light. LED light ring with 16 switchable lamps for adjustable light from the top. Long stand. Camera 12 MP, 60 fps, computer with Las X software. This microscope is in the greenhouse on floor 2 at the photo station.
Stereomicroscope Leica M125C at UPSCScreening stereomicroscope Leica MZ9.5
This microscope is suitable for fast screening and basic imaging, equipped with CCD camera MC190HD and LAS EZ software. The system is in the greenhouse on floor 4.
Stereomicroscope Leica MZ9s at UPSCBasic stereomircroscope Leica M16
This stereomicroscope is suitable for screening in wilde field. The system is located in the greenhouse on floor 4.
Stereomicroscope Leica MZ16 at UPSC
Crossing stereomicroscope, Zeiss Stemi 2000-C
This basic stereomicroscope is suitable for crosses. The system is in the greenhouse on floor 4.
Stereomicroscope Zeiss Stemi 2000 C at UPSC