A compound microscope looks through thin, backlit samples at high power. A stereo microscope shows whole objects in 3D at low power, with room to work under the lens.
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One looks through thin slides, the other at whole objects.
The short answer
Choose a compound microscope for cells, bacteria, pond water and prepared slides. Choose a stereo microscope for insects, seeds, flowers and anything you want to move while you watch.
AmScope's comparison draws the same line: compound for transparent specimens at high magnification, stereo for opaque, three-dimensional objects.
Side by side
Compound microscope
Stereo microscope
What you look at
Thin, transparent samples on a slide
Whole, solid objects
Magnification
40X, 100X, 400X and 1000X with a 10X eyepiece
20X to 80X on the SE306R-PZ, 3.5X to 90X on the SM-4TZ-144A
Image
One light path, split to both eyes
A separate path for each eye, seen in 3D
Working distance
0.14 to 4 mm
53 mm on the SE306R-PZ
Light
From below, through the sample
From above, and often from below too
Genetics projects
Cheek cells, onion root tip mitosis, stained bacteria
Sorting fruit flies, counting corn kernels, looking at colonies on a plate
Why a compound microscope can't do a stereo's job
A compound objective sits very close to the sample. AmScope gives compound working distances of 0.14 to 4 mm, which leaves no room for tweezers or a fly.
Light has to pass through the sample, which is why specimens are sliced thin or spread on a slide. A whole insect is too thick and too opaque to see this way.
A stereo microscope sends a slightly different image to each eye, and MicroscopyU explains how the brain combines the two into depth.
Why a stereo microscope can't do a compound's job
Cell detail needs the 400X to 1000X that a compound microscope reaches with its 40X and 100X objectives. AmScope lists bacteria, plant cells and chromosomes as compound work.
Some stereo microscopes have a light under a frosted glass stage, so a slide can go on them. At 80X that shows a whole slide, not what is inside the cells.
One of each
The AmScope SE306R-PZ is a pillar-stand stereo microscope with 2X and 4X objectives and WF10X and WF20X eyepieces, for 20X, 40X and 80X. It has a light above and a light below the stage.
The AmScope B120C-E1 is a binocular compound microscope rated 40X to 2500X, sold with a 1MP USB camera that goes in place of an eyepiece.
That 2500X figure comes from pairing the 100X objective with 25X eyepieces. Leica calls magnification past a system's resolving power empty magnification, and with a 1.25 NA objective the useful ceiling is about 1250X (1000 times the NA). Judge these microscopes on their objectives.
For more range, the SM-4TZ-144A zooms from 3.5X to 90X on a boom stand, and the Swift SW380T adds a camera port to a compound microscope.
Compound, binocular
AmScope B120C-E1 binocular microscope with camera
Binocular compound microscope, 40X to 2500X, with a Siedentopf head. The 1MP USB camera sits in an eyepiece tube in place of an eyepiece. There is no photo port.
Binocular pillar-stand stereo microscope at 20X, 40X and 80X, with 2X and 4X objectives, lights above and below the stage and a 53 mm working distance.
Start from the project. Fruit fly crosses are sorted under a stereo microscope. Stained slides of cheek or onion cells need a compound one.
If you plan to photograph what you see, check the camera options first. Microscope camera adapters covers which models take which cameras.
Common questions
A compound microscope magnifies thin, backlit samples on slides, usually 40X to 1000X. A stereo microscope shows whole objects in 3D at lower power, with room to work under the lens.
It depends on what you want to see. Cells and bacteria need a compound microscope. Insects, plants and fruit flies are easier under a stereo microscope.
Not in detail. Cell structures need the 400X to 1000X of a compound microscope, and the SE306R-PZ tops out at 80X.
Yes. AmScope notes that stereo microscopes are also called dissection or dissecting microscopes.
A stereo microscope. Sorting flies by eye color and wing shape takes low power, a 3D view and room to move the flies.