ASCENT Troubleshooting Guide

General Troubleshooting Steps

  • Check your geometry (ascent/samples/sample_index/models/model_index/debug_geom.mph)

  • Check your sample (ascent/samples/sample_index/slides/cassette_index/slide_index/masks)

Installation Issues

  • NEURON

    • issue: Sometimes NEURON installation will complete but NEURON will not be installed

    • solution: Run the installer in Windows 8 compatibility mode

Pipeline Issues

  • Sample

    • issue: Small white pixel islands cause the pipeline to fail, or the pipeline does not fail but very small elements are present as fascicles that reflect segmentation errors

    • solution: increase value of image_preprocessing>object_removal_area in sample.json

  • Model

    • issue: fascicle borders appear ragged/wavy in model geometry

    • solutions:

      • Increase inner_interp_tol and/or outer_interp_tol in sample.json (depending on whether the issue exists for outers or inners)

      • If your mask is very pixelated, increase smoothing>fascicle distance in sample.json

NEURON Issues

Issue: Compiling NEURON files with python submit.py results in an error, mpicc: command not found Solution: Install open-mpi 2.0 and add to path

Python Issues

  • issue: python output prints out of order with java output

  • solution: pass the -u flag (i.e. python -u run pipeline ), which turns off output buffering