In general, we prefer to return samples to Earth for analysis. There are many benefits: no need to haul instrumentation into orbit, plenty of storage/time/personnel/equipment for analysis, and easier to modify or expand experiments. When instrumentation is brought into space, it typically is for one of the following justifications:
- It is measuring something at that particular location (e.g. radiation, pictures of a planet's surface) which can't be "brought back".
- It is needed for or by the astronauts (e.g. biotelemetry, monitoring of cabin conditions).
- It measures the progress of a phenomenon over time (e.g. cell growth, astronaut weight).
- A sample would be altered or destroyed by its return to Earth (e.g. fluid experiments).
Skylab had a handheld optical microscope. It was used to examine the growth of bacteria and fungi in space, cytoplasmic streaming in Elodea, and the behavior of antibodies in a weightless environment. A camera was attached to the microscope in some experiments.
There are references to microscopes in the Spacelab module aboard the Space Shuttle. However, not enough details are given to determine the types of these instruments.
The International Space Station has had a variety of microscopes on board. One is a fairly traditional optical scope:
The Saibo Rack (Saibo) [JAXA] is a multi-purpose rack consisting of two main parts, the Clean Bench (CB) and Cell Biology Experiment Facility (CBEF). The primary purpose of the Saibo Rack is to support cell culture, plant culture and mouse projects across a range of life and biological sciences.
The CB is a sterilized glovebox equipped with a phase contrast micro- scope. The microscope has different modes: Bright-Field, Phase-Contrast and Fluorescence Microscope, and the objective lens can be switched among four magnification levels.
A second is a more sophisticated fluorescence microscope:
The JAXA Microscope Observation System (Fluorescence Microscope) [JAXA] is located in the MSPR or in the cabin area. It is an inverted fluorescence microscope, a Leica DMI 6000B. It has 6 different objective lenses, with a monochrome CCD camera. The microscope is equipped with an LED illumination unit and can perform time-lapse videomicroscopy. It also is equipped with a stage heater (up to 40°C) to enable cell culture observation. The Fluorescence Microscope is controlled and remotely commanded from the ground once samples are placed into it by the onboard crew. It has been used for biology (cultured cell and fish larva) and plant experiments onboard the ISS/Kibo.
A third is an optical microscope designed mainly for observing fluids, though it has been used for other purposes:
Fluids Integrated Rack (FIR) [NASA] is a multi-user fluid physics research facility designed to accommodate and image a wide variety of microgravity fluid experiments.
An additional component of the FIR that is itself considered a multipurpose facility is the Light Microscopy Module (LMM) [NASA], a ground-controlled, automated microscope that allows flexible imaging (bright field, dark field, phase contrast, etc.) for physical as well as biological experiments.
Source: International Space Station Facilities: Research in Space 2017 and Beyond
A confocal/3D scope launched in April 2018 may be the closest to what you are looking for:
Depending on the sample, Microscopy SpaceLab also offers selectable specialized techniques to improve specimen contrast, or highlight specific structures utilizing polarization, Differential Interference Contrast (DIC) or 3D capabilities in multiple illumination modes. Microscopy SpaceLab is equipped with 8 selectable objectives ranging in magnification from 2X-100X, 7 selectable laser excitation wavelengths and an array of dichroic and emission filters to accommodate a variety of fluorescence imaging options. Confocal functionality will be implemented with selectable laser illumination optics and pinhole system utilizing the same scientific camera sensor as the other operational modes, thus maintaining a compact form factor. In addition, confocal scanning to obtain 3D imaging and depth information is implemented utilizing HNu’s patented illumination and imaging operations that are much more amenable to compact integration within the system.
Two additional off-the-shelf scopes were added in July 2018:
The NanoRacks Microscopes facility includes commercial off-the-shelf optical and reflective microscopes. NanoRacks Microscopes utilize plug-and-play USB technology and allow crew members to analyze and digitally transfer images of International Space Station (ISS) on-orbit samples.
All of the ISS scopes have used imaging sensors. None use charged particles. The Microscopy SpaceLab is the only scanning scope. Though they are all fairly advanced optical microscopes, none would be considered an electron microscope.