Folder structure

To load data into Cell-ACDC you need to structure the files in a specific way.

In the section Creating Data Structure we explain how to achieve this in an automatic fashion.

Here, instead we will focus on how the folder structure should look like.

Important

We do not recommend creating the folder structure manually. Here we only want to provide more details about how the folder structure look like. To create the folder structure automatically from a microscopy file use either module 0 of Cell-ACDC (explained here Creating Data Structure) or Fiji macros that you can find here <https://github.com/SchmollerLab/Cell_ACDC/tree/main/FijiMacros>_.

In Cell-ACDC we refer to the folders with two names:

  1. The experiment folder with an arbitrary name

  2. The position folder with names like Position_1, Position_2, etc.

The experiment folder is a folder that typically identifies a specific experiment and it contains one or more position folders.

The position folder is a folder inside the experiment folder that must contain a folder called Images. In Cell-ACDC we refer to “positions” with the same meaning of the term “series” in ImageJ/Fiji. These are also called “Tiles” by some microscopy manufacturers. You can have as many position folders as you like in each experiment folder.

The Images folder contains the image files. You will need to create one TIFF file per channel. Each TIFF file can be 2D, 3D (z-stack or 2D over time), or 4D (z-stack over time). You can have as many channels as you want.

The filenames of each file must all start with the same <basename>, which is a text that is common to all the files in the folder.

This is probably more clear with an example. Let’s say that you have an experiment called mitochondria_medium_switch with 5 positions and each position has three channels: phase_contrast, GFP, and mCitrine. With this structure you create a folder called mitochondria_medium_switch and inside this folder you create 5 folders, one for each position, called Position_1, Position_2, …, and Position_5. Inside each position folder you create a folder called Images. Inside each Images folder you create the TIFF files, one for each channel, all starting with the same basename. The basename is a text that allows you to identify what the experiment is about, for this example we will use the basename ASY015_mitochondria_medium_switch_.

In this hypothetical example, the folder structure wood look like the following:

mitochondria_medium_switch
├── Position_26
│    └── Images
│       ├── ASY015_mitochondria_medium_switch_metadata.csv
│       ├── ASY015_mitochondria_medium_switch_GFP.tif
│       ├── ASY015_mitochondria_medium_switch_mCitrine.tif
│       └── ASY015_mitochondria_medium_switch_phase_contrast.tif
│
├── Position_2
│    └── Images
│        ...
│
├── ...
│
└── Position_5
    └── Images
        ...

You probably have noticed an additional file that ends with _metadata.csv. If this file is missing it will be created by Cell-ACDC. It contains useful metadata like the pixel size and other metadata, but it also contains an entry called basename. If you don’t create this file Cell-ACDC will try to guess the basename from the filenames. While this usually works fine, it is better to create this _metadata.csv file with the following content:

Description,values
basename,ASY015_mitochondria_medium_switch_

This way Cell-ACDC will not try to guess the basename and you will avoid weird naming of additional files due to the wrong basename being guessed.