starfish: `write_experiment_json()` doesn't handle non-flat experiment directory structures correctly

Hi all,

So I’ve encountered an issue when running write_experiment_json() in ‘no copy’ mode (see: https://github.com/spacetx/starfish/pull/1053)

The resulting output .json files that starfish produces all assume that image tiles reside in the experiment root directory (see: https://github.com/spacetx/slicedimage/blob/3456f86a10cc9c89996a394cb75a03457a9bf6bc/slicedimage/io.py#L303).

However, our data (and likely many other group’s data) do not live in a flat directory structure. Ours happens to look like:

expt_root_dir
| - Round_1_dir
|    | - FOV_1_dir
|    |   | - channel_1_z_1.tiff
|    |   ...
|    | - FOV_2_dir
|    |   | - channel_1_z_1.tiff
|    |   ...
|    ...
| - Round_2_dir
|   | - FOV_1_dir
|   |    | - channel_1_z_1.tiff
|   |    ...
|   ...
...

Although this issue arises because Starfish can no longer dictate a flat data structure (by forcing copying), copying has to be optional as the overhead of creating a new copy of huge ‘local’ datasets is unreasonable.

From an end-user perspective, having image data organized into subdirectories is also much easier to deal with than having to deal with one folder with thousands of tiffs.