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12 changes: 8 additions & 4 deletions DeepProfiler-Handbook/docs/04-metadata.md
Original file line number Diff line number Diff line change
Expand Up @@ -38,15 +38,19 @@ view. The following list indicates the minimal columns that the metadata file is
(i.e., colors) and DeepProfiler assumes that each channel is stored in a separate image file (all channels stored in
the same file are not currently supported). Therefore, to put together all the channels of a single image, the metadata
file will need to have multiple _channel_name_ columns listed in the configuration file. These columns can be renamed as
necessary and should point to the corresponding image files using a path relative to the image directory. For example,
an assay with DNA, RNA, and Mito stains will have three channel columns named accordingly, with entries in each column
necessary and should point to the corresponding image files using a path relative to the image directory. For example, an assay with DNA, RNA, and Mito stains will have three
channel columns named accordingly, with entries in each column
pointing to the corresponding image file. The field may have different names.
5. `Treatment`: We assume that cells in a well have been treated in a biologically meaningful way or represent different

- **Image path (default)**: The images can be located in the default DeepProfiler folder (which is `inputs/images`) so no specific path needs to be defined here, only the Plate/FileName, as shown in the [metadata file example](https://github.com/cytomining/DeepProfiler-handbook/blob/00f3b41e753a40a1e3854a75bd491b7c1864a4da/DeepProfiler-Handbook/assets/index.csv).
- **Image path (customized)**: If the user cannot move the images to the default location, images can also be located in a specific folder inside the user's machine instead of the default. For example, a user can specify the location of the DNA image to be `C:\Users\User1\images\41744\taoe005-u2os-72h-cp-a-au00044859_f21_s1_w159ff0023-3fa4-4acb-a277-af596b4e9e25.tif`.

6. `Treatment`: We assume that cells in a well have been treated in a biologically meaningful way or represent different
experimental conditions. This column keeps track of that information, which may have other names (in the provided example
data, it is called `pert_name`). It is useful as an identifier of the type of biological experiment, treatment, perturbation
or condition of cells observed in the images. This column must be a biologically meaningful label that could be used by
DeepProfiler for training purposes. May have different names.
6. `Replicate`: Number or identifier indicating which repetition of the treatment an image corresponds to. In the provided
7. `Replicate`: Number or identifier indicating which repetition of the treatment an image corresponds to. In the provided
example data this column is called `pert_name_replicate`.

These are the minimum columns required in the metadata file. You can append more columns with information specific to your
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