Recommended folder structure

Based on typical VIEW workflows, the following folder structure is recommended. This would be the structure for a project and leads to easier reproducibility and archiving:

project directory (name is flexible, referred in VIEW as: STG_MotherOfAllFolders)
│   
|    analysis1.yml
|    analysis2.yml
|    .............
|
└─── data (name is flexible, referred in VIEW as: STG_Datapath)
│    |   Animal 1 data file/folder
│    |   Animal 2 data file/folder
|    |  ........................
│   
└─── progs (name is flexible)
|    |   script 1
|    |   script 2
|    |   .......................
|
└─── lists (name is flexible, referred in VIEW as: STG_OdorInfoPath)
|    │   
|    │   Animal 1 list file
|    |   Animal 2 list file
|    |  ........................
|
└─── coor (name is flexible, referred in VIEW as: STG_OdormaskPath)
|    |   Animal 1 coor file
|    |   Animal 2 coor file
|    |   .......................
|
└─── output (name is flexible, referred in VIEW as: STG_OdorReportPath)
     |   File 1
     |   File 2
     |   .......................
 

The project directory contains everything about a single experimental series (one scientific question). This will consist of many animals/preparations being measured. Every animal has an individual and unique tag. Ideally of the sort Person_Experiment_DateLetter, e.g. LM_GC-FID_or22a_170726c.

Folder Data contains everything that comes from the setups - i.e. all raw data, no processing done. Typically, all measurements of one animal are in one folder with the name animal.

Folder Lists contains all info for metadata, i.e. what is written in the lab book, in a standardized tabular format. Typically, all info about one animal is in one file containing one line per measurement. File extensions vary with format, e.g. animal.settings or animal.lst or animal.lst.xls. This folder may also contain a list of all animals.

Folder Coor contains all info about space, i.e. position of the brain tissue, position of individual somata, position of glomeruli. Formats vary for different tasks, or for different ways to define these positions. For example, animal.coor; animal.Area; animal.coor_mask.tif; animal.coor.roi; animal.roi

Folder Progs contains the python scripts for data analysis. Typically, a script contains the instructions of: 1) which .yml file to use (setting the flags, i.e. deciding on filter, data calculation, data output format, etc.) 2) which animals to process.

Folder Output contains all the output created by the scripts. A good script will copy itself and the .yml file into the output folder. If this is the output that you need, you would rename the folder and keep it (e.g. "Output_rawData_noFilter", "Output_filter3_bleachCorrected" ... ). Typical output formats are: overviews (single frame analysis of every measurement), movies and glodatamix files. Glodatamix files can be processed in python, e.g. notebook, or in R.