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. Author manuscript; available in PMC: 2013 Jul 4.
Published in final edited form as: Nat Protoc. 2012 Jan 12;7(2):193–206. doi: 10.1038/nprot.2011.439
Step Problem Possible Cause Solution
1C Brain is soft rather than hard Poor perfusion Discard, try another animal
Brain appears bloodied Discard, try another animal
Liver does not turn pink Discard, try another animal
Fixation solution coming out of the nose or mouth of animal Discard, try another animal Use ideal perfusion pressure (~150 mmHg)
1, 2, 43 Tissue dark and murky looking, uneven membranes Poor initial fixation, unhealthy tissue Use only healthiest tissue for experiments, If poor perfusion or sick animals, discard. Use fresh fixatives only
Inadequate rinsing between osmication and TCH treatment Rinse well before and after osmium and TCH steps.
23, 25 Block chipping or tissue falling out of section Inadequate infiltration Be sure to infiltrate overnight on rotator for 2 nights
Using EM trimmer blade too fast Approach block slowly
Block center soft Inadequate infiltration Longer infiltration, use only freshly prepared resins for infiltration and embedding
28.32 Ribbon curves Top and bottom of block face not parallel, uneven sides Re-trim block with fresh razor blade or diamond trimming tool
29 Ribbon not sticking together Not enough glue on top and bottom of block face Add more glue to top and bottom of block face
44 Charging of specimen in SEM Not enough carbon coating or copper tape on coverslips Remove sample and try more tape or carbon coat the surface
Beam damage, breaks in section Beam too bright Try using lower voltage, reduce kV and brightness
Bubbling of sections, black blobs forming Sections have too much moisture Allow sections to air dry then store under vacuum for 24 hours
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