SUGGESTIONS FOR SECTIONING PARAFFIN BLOCKS
WITH A ROTARY MICROTOME
1. Make certain the knife is sharp.
2. Cut paraffin block in the shape of a trapezoid. Mount the shortest axis
of the block parallel to the long axis of the knife.
3. For a paraffin ribbon of sections to be straight, the top and bottom of
the paraffin block and the edge of the knife must be parallel. The
obliques sides of the block must also be cut on the same angle
respective to one another otherwise the sections will curve to one side
as they come off the knife.
4. After the paraffin block is mounted and the knife is in place, recheck all
screws to be sure each is tight.
5. After sectioning collect the ribbons and place gently them in the warm
(45 °C ) water bath. Ribboins should be kept in the water bath no
longer than 2 minutes.
6. Prepare a clean microscope slide. Dip it in 100% alcohol and dry with a
Kimwipe. Mark slides with a glass-marking pencil.
7. WATER BATH method:
 Place the sections on top of the water (45 oC).
 When the sections are completely expanded, float them on top of
a slide and remove from water bath. Store slides at an angle until
completely dry.
8. Once completely dry baking sections onto the slides by placing them in
the large convection oven at 65 °C for 25 minutes or until most of the
paraffin wax is melted to the slide.
9. Cool slides before putting them away in the slide compartment.
TROUBLE-SHOOTING HINTS
SYMPTOM
Bubbles in paraffin block
Block is brittle when sectioned
Sections compress during
sectioning, i.e., section is
considerably smaller than block
face
Chatter (alternating light & dark
lines in sections, parallel to knife)
Alternate thick and thin sections
Curling
Ribbons curved
Tissue falls out of sections or
crumbles
Sections or ribbons stick to knife
or block face
Ribbon wrinkled on microscope
slide
Crooked ribbons on microscope
slide
Bubbles under paraffin sections
PROBABLE CAUSE(S)
 Paraffin bubbled when applied to
disposable embedding mold
 Paraffin heated above its melting point
 Block (or knife) is too warm
 Residual alcohols in tissue
 Dull knife
 Section thickness is too thin
 Knife or block not rigidly clamped
 Dull knife
 Knife or block not rigidly clamped
 Block is too soft
 Knife or block is not rigidly clamped
 Microtome faulty
 Paraffin too hard (temperature too low)
 Paraffin section too think
 Atmospheric conditions – too humid
 Knife angle is too steep
 Top & bottom block face not parallel
 Lower edge of paraffin block not parallel
to knife edge
 Poorly cut trapezoid
 Tissue of irregular shape or bulk
 Poorly infiltrated tissue due to:
1. Incomplete removal of fixative
residues
2. Incomplete dehydration & infiltration
steps (too short)
3. Insufficient volume of liquid used
4. Tissue composition resists infiltration
 Dull knife edge
 Static electricity
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Insufficient time on water bath
Ribbon not picked up properly from bath
Curved ribbons due to poor trimming of
block
Jagged edges of sections catch other
edges because ribbons are placed too
close together
Air bubbles in water bath not removed
Warming bath too hot (above 45oC)