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Last edited by Christian Evenhuis

Using naming conventions

Up: Organising data

A good naming convention helps keep your data organised. Some scripts have been added to OMERO to help extract metadata from file names as key-values pairs.

Key-value pairs are a very flexible way to record the meta data associated with your data. OMERO has powerful searching functions that allow you to search the metadata attached to the files.

Naming conventions

  1. Don't use whitespace.
  2. Record the important variables (values) in the file name
  3. Separate variables (values) in filenames or directories by an underscore (_)
  4. You can use directory structure to organise your data, the management of this is a little more complicated though.

Guidelines

There are no specific rules how to name your files. Whatever system you choose to use, they should be detailed enough that someone from your research group could take your lab book and identify what each image is.

  • More detail is better: Adding some hints, like time or cell-line makes it easier for you, and others, to at a glance work out what the naming system means.

  • Too much detail is bad: Really long filenames are annoying to type and have higher chance of typos. If the names get really long Windows cannot deal with them.

  • Directories can help: You may prefer to organise your data into directories. This helps to reduce input errors. After importing to OMERO there are some scripts that add the directories to the filename.

Each research group has different priorities so it is a good idea to discuss with your team what is the key information that should be included in your naming system.

Examples

Here are some example of filenames:

171101_dose-100_time1_rep1.tif

  • date of experiment
  • dose
  • time in hours since the start of the experiment
  • replicate number

20161207_Lforms_pre2PFA_Control_4A02_R3D.dv

  • date of experiment
  • substrate shape
  • step in treatment
  • the treatment
  • a locate code for the field of view

2017_HardballCochlear/R3/1_8/01_R3D.dv

This one uses directory structure to help organise the images

  • name of trial
  • code for the substrate (R3)
  • field of view code (1_8)
  • replicate number (01)