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| Problems | Possible reason | Solutions |
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| Spinal cord destroyed during chopping | The tissue is too soft | All the procedures must be done on ice and the chopper table should be chilled before cutting |
| The blade cuts too fast and tears the tissue up | The blade speed should be approximately adjusted to make a single cut every single second |
| The blade does not stick closely to the chopper table | Make sure that the blade tightly sticks to the chopper table |
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| Aberrant axonal projections | The spinal cord is not placed in a parallel-to-the-blade fashion | Before cutting check whether the spinal cord is set parallel to the blade. |
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| Slices die after 1 week | Incorrect pH of the medium | pH must be adjusted to 7.2 each time the medium is changed |
| The precutting procedure takes too much time | The whole procedure should not take more than 90 min (from decapitating animals up to placing the slices onto the membrane) |
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| Transplanted cells die after short time | The density of the transplanted cells is too high | Try different amount of cells |
| The cells are not evenly suspended | Before transplantation mix cells in eppendorf with pipette gently but precisely |
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| Slices and cells detach from the membrane during fixation | PFA was old or too cold | After preparing PFA solution do not freeze the preused doses and before fixation heat PFA up to 37°C |
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| Slices are not evenly stained | The permeabilization is too weak or too short | Add Triton-X 0.2% to the primary antibody solution |
| The slice was not completely covered with liquid | Using a brush or tips let the slice gently sink to the bottom of the well; it should stay there during entire staining procedure |
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| The slice structure is destroyed during slide closing | The coverslip is too heavy and crushes are rich in lipids structure | Add a double portion of mounting medium and wait a while until it dries a little before applying coverslips |
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