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incomplete paraffin removal can be caused by
insufficient time in xylene, water contamination in xylene, paraffin contamination in xylene
How to fix insufficient time in xylene during rehydration step
Treat with xylene x3, then 100% alcohol x3 and then decolorize with acid alcohol
How to fix slide after water has been left on the slide during the drying step resulting in contaminated xylene
Treat with absolute alcohol to dehydrate, then put into xylene to complete deparaffinization and then continue with rehydration step
What can cause uneven staining
Insufficient reagent levels, thick and thin sections when tissue was cut, inadequate processing due to water contamination
How to fix a slide that has been processed with insufficient reagent levels
Decolorize and restain
How to fix a slide that has thick and thin sections in the tissue from being cut
Troubleshoot microtome, recut and stain slide
How to fix a slide that has inadequate processing due to water contamination
Can attempt reprocessing but it is hard on the tissue
What causes water and slides to be milky after the deparaffinization step
Presence of xylene/formula 83 on the slides
How to fix slides that are milky after deparaffinization step
Reverse process the slide
What causes smudgy nuclear staining
Incomplete fixation, overheating of tissues
How do you fix a slide where the tissue has been incompletely fixed
Unable to fix
How do you fix tissue that has been over hardened
If it is a slide issue, recut and restain. If it is a problem with embedding, see if there is more sample left over to reprocess properly
What causes pale nuclear staining
Insufficient time in hematoxylin, hematoxylin is depleted, over differentiation with acid alcohol, section is too thin
How to fix a slide that has insufficient time in hematoxylin
Restain for the correct amount of time
How to fix a slide that has been over differentiated
Restain
What causes dark/overstrained nuclei
Too long in hematoxylin, under differentiation with acid alcohol, section is cut too thick
What causes nuclei to be red
Overoxidized hematoxylin, improper bluing,
What causes nuclear bubbling
Improper fixation, rushed oven drying of cut slides before staining
What causes pale cytoplasmic staining
pH of eosin is too high, over exposure to dehydrating alcohols or section is cut too thin
How to restore the pH of eosin
Adjust pH to 4.1-4.5 with acetic acid
What causes no eosin differentiation
Slide is not in dilute alcohols long enough after eosin, improper fixation, eosin has the improper pH
What causes cytoplasmic staining to be too dark
Eosin is too concentrated, section was left in eosin for too long, section was not in dilute alcohols long enough after eosin, section is cut too thick
What causes precipitate on top of sections
Precipitate in hematoxylin, possible formalin pigment
How to fix precipitate in hematoxylin
Filter stains before use
How to fix possible formalin pigment
Remove with alkaline alcohol or alcoholic picnic acid, decolorize and restain the slide
What causes water bubbles under the coverslip
Slides not completely dehydrated before clearing in xylene
What causes areas of the slide to be unfocused
Mounting media on top of coverslip, coverslip was not applied with good technique
What causes cloudiness under the coverslip
Water contamination in xylene
What causes “cornflaking” on the slide
Tissue partially dries before the coverslip is applied
What causes retracting mounting media
Warped coverslip, mounting media is too thin, air is trapped under the section