File comes up black in ImageMagick but shows fine in ImageJ does anyone know why? It is 16 bit grayscale

For 16 bit grayscale, we may use auto-level option:

image.AutoLevel();

Assume your PC supports only 8 bits grayscale display (in RGB format, the grayscale is displayed as 8 bits per red, green and blue, when r=g=b for each pixel).

When we want to display a 16 bits image, we have to convert it to 8 bits first.
The default conversion used by your viewer is getting the upper 8 bits of every 16 bits, and ignoring the lower 8 bits (equivalent of dividing all pixels by 256).

In case the pixels range is about [0, 255] for example (or say [0, 1000]), the image is going to be very dark, or entirely black.
In your case, the pixels range is probably low, so the displayed image looks black.

The "auto-level" processing, adjusts the pixel range using "linear stretching".
Finds the minimum and the maximum pixel values, and applies scale and offset that brings the minimum to 0 (black) and the maximum to 255 [or 65535 for 16bits] (white).

For correctly handling 16 bit images, we have to install Magick.NET-Q16.
See the following post for details.

For testing, I used the oldest release of MagickViewer.

Added the following code:

//Update for automatic ajusting the 16 bits image for display
////////////////////////////////////////////////////////////////////////////
foreach (var image in Images)
{
    image.AutoLevel();
}
////////////////////////////////////////////////////////////////////////////

Complete testing code:

//=================================================================================================
// Copyright 2013-2014 Dirk Lemstra <https://magickviewer.codeplex.com/>
//
// Licensed under the ImageMagick License (the "License"); you may not use this file except in 
// compliance with the License. You may obtain a copy of the License at
//
//   http://www.imagemagick.org/script/license.php
//
// Unless required by applicable law or agreed to in writing, software distributed under the
// License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either
// express or implied. See the License for the specific language governing permissions and
// limitations under the License.
//=================================================================================================
//https://github.com/dlemstra/MagickViewer/tree/6.8.9.501

using System;
using System.Collections.Generic;
using System.Diagnostics.CodeAnalysis;
using System.IO;
using System.Linq;
using System.Threading;
using System.Windows.Threading;
using ImageMagick;
using Microsoft.Win32;

namespace MagickViewer
{
    //==============================================================================================
    internal sealed class ImageManager
    {
        //===========================================================================================
        private static readonly object _Semaphore = new object();
        private static readonly string[] _GhostscriptFormats = new string[]
        {
            ".EPS", ".PDF", ".PS"
        };
        //===========================================================================================
        private Dispatcher _Dispatcher;
        private OpenFileDialog _OpenDialog;
        private SaveFileDialog _SaveDialog;
        //===========================================================================================
        private void ConstructImages()
        {
            if (Images != null)
                Images.Dispose();

            Images = new MagickImageCollection();
        }
        //===========================================================================================
        [SuppressMessage("Microsoft.Globalization", "CA1308:NormalizeStringsToUppercase")]
        private static string CreateFilter(IEnumerable<MagickFormatInfo> formats)
        {
            string filter = "All supported formats (...)|*." + string.Join(";*.",
                                            from formatInfo in formats
                                            orderby formatInfo.Format
                                            select formatInfo.Format.ToString().ToLowerInvariant());

            filter += "|" + string.Join("|",
                                            from formatInfo in formats
                                            orderby formatInfo.Description
                                            group formatInfo.Format by formatInfo.Description into g
                                            select g.Key + "|*." + string.Join(";*.", g).ToLowerInvariant());
            return filter;
        }
        //===========================================================================================
        private void Initialize()
        {
            _OpenDialog = new OpenFileDialog();
            SetOpenFilter();

            _SaveDialog = new SaveFileDialog();
            SetSaveFilter();
        }
        //===========================================================================================
        private void OnLoaded()
        {
            if (Loaded == null)
                return;

            _Dispatcher.Invoke((Action)delegate()
            {
                Loaded(this, EventArgs.Empty);
                Monitor.Exit(_Semaphore);
            });
        }
        //===========================================================================================
        private void OnLoading()
        {
            if (Loading != null)
                Loading(this, EventArgs.Empty);
        }
        //===========================================================================================
        private void ReadImage(FileInfo file)
        {
            ConstructImages();

            try
            {
                MagickReadSettings settings = new MagickReadSettings();
                if (_GhostscriptFormats.Contains(file.Extension.ToUpperInvariant()))
                    settings.Density = new MagickGeometry(300, 300);

                Images.Read(file, settings);
                FileName = file.Name;

                //Update for automatic ajusting the 16 bits image for display
                ////////////////////////////////////////////////////////////////////////////
                foreach (var image in Images)
                {
                    image.AutoLevel();
                }
                ////////////////////////////////////////////////////////////////////////////
            }
            catch (MagickErrorException)
            {
                //TODO: Handle error
            }

            OnLoaded();
        }
        //===========================================================================================
        private void Save(string fileName)
        {
            Images.Write(fileName);
        }
        //===========================================================================================
        private void SetOpenFilter()
        {
            var formats = from formatInfo in MagickNET.SupportedFormats
                              where formatInfo.IsReadable
                              select formatInfo;

            _OpenDialog.Filter = CreateFilter(formats);
        }
        //===========================================================================================
        private void SetSaveFilter()
        {
            var formats = from formatInfo in MagickNET.SupportedFormats
                              where formatInfo.IsWritable
                              select formatInfo;

            _SaveDialog.Filter = CreateFilter(formats);
        }
        //===========================================================================================
        public ImageManager(Dispatcher dispatcher)
        {
            _Dispatcher = dispatcher;

            Initialize();
        }
        //===========================================================================================
        public event EventHandler Loading;
        //===========================================================================================
        public event EventHandler Loaded;
        //===========================================================================================
        public string FileName
        {
            get;
            private set;
        }
        //===========================================================================================
        public MagickImageCollection Images
        {
            get;
            private set;
        }
        //===========================================================================================
        public static bool IsSupported(string fileName)
        {
            if (string.IsNullOrEmpty(fileName))
                return false;

            if (fileName.Length < 2)
                return false;

            string extension = Path.GetExtension(fileName);
            if (string.IsNullOrEmpty(extension))
                return false;

            extension = extension.Substring(1);
            MagickFormat format;
            if (!Enum.TryParse<MagickFormat>(extension, true, out format))
                return false;

            return (from formatInfo in MagickNET.SupportedFormats
                      where formatInfo.IsReadable && formatInfo.Format == format
                      select formatInfo).Any();

        }
        //===========================================================================================
        public void Load(string fileName)
        {
            Monitor.Enter(_Semaphore);

            OnLoading();

            Thread thread = new Thread(() => ReadImage(new FileInfo(fileName)));
            thread.Start();
        }
        //===========================================================================================
        public void ShowOpenDialog()
        {
            if (_OpenDialog.ShowDialog() != true)
                return;

            Load(_OpenDialog.FileName);
        }
        //===========================================================================================
        public void ShowSaveDialog()
        {
            if (_SaveDialog.ShowDialog() != true)
                return;

            Save(_SaveDialog.FileName);
        }
        //===========================================================================================
    }
    //==============================================================================================
}