Add ImagedSlice entity to In Vitro Slice Neuron Morphology Reconstruction schema

[jmbudd]

In the process of applying Neuroshapes In Vitro Slice Neuron Morphology Reconstruction schema to the curation of combined anatomical and electrophysiolgical slice data from mouse hippocampus, I encountered a number of issues. Since these issues may well arise during the curation of similar datasets for other labs, I thought it might be useful to share them here. I have created a separate ticket for each issue. (This introductory paragraph is repeated in each.)

A confocal microscopic image stack is commonly used to record single cell labelling through the depth of the slice. To reconstruct a neuron's morphology, the image stack is then explored, typically manually, to trace and connect labelled processes to the same cell body. But the current Slice schema does not appear to have an entity for incorporating these raw data. A VolumeImageStack entity does exist but it does not appear to have any listed attributes and is not currently part of the publicly documented Slice schema. Though image stack files are large (Gbs) they ought to be included in curation consistent with FAIR principles to allow others to reuse and reanalyse the raw experimental data, e.g. applying automated tracing algorithms.

To address this issue, I created, consistent with Slice schema naming, an ImagedSlice entity that records basic information about data collection (e.g. protocol details the microscope used and its settings) and a list of the files generated (frequently there is more than one image stack file per neuron reconstruction), i.e. in yaml format:

ImagedSlice:
  protocol:
  person:
  date:
  name:
  generated:
  comment: