Data¶

Please note that we recommend a data organization, described below, to facilitate the usage of these tools.

We provide test data, which allows you to inspect how the data is organized, but then also run a local installation of these tools to see if everything works correctly.

Test data¶

Already processed test data can be downloaded from Dropbox. With these data, you can verify if the different analysis steps are properly executed.

Data organization¶

We strongly recommend the following data-organization on which this workflow has been tested.

1. Images are store as single-channel multi-z-stack tif files, e.g on tif per position and channel. If your data are not single-channel, see the section on how to split channels with Fiji.
2. All raw 3D images are stored in a folder acquisition
3. All analysis results are stored in subfolder analysis, where each analysis step has a separate subfolder.

The organization of the provided test data is the following

├─ example_data/
│  ├─ acquisition                          # Folder with raw data
│  │  ├─ test_pos001_cy3.tif
│  │  ├─ test_pos002_dapi.tif
│  │  ├─ test_pos002_cy3.tif
│  │  ├─ test_pos002_dapi.tif
│  ├─ analysis                              # Folder with all analysis results
│  │  ├─ segmentation-input                 # Folder with projected images for segmentation 
│  │  │  ├─ img-prop__test_pos001_cy3.json  # json file with image properties
│  │  │  ├─ test_pos001_cy3.png             # Projected image
│  │  │  ├─ ....
│  │  ├─ segmentation-results               # Folder with segmentation results 
│  │  │  ├─ test_pos001_cy3.tif
│  │  │  ├─ test_pos001_cy3.tif
│  │  │  ├─ test_pos001_cy3.tif
│  │  │  ├─ ....
│  │  ├─ ....
│  │  ├─ FQ_outline                         # [Optional] FQ outlines 
│  │  │  ├─ test_pos001_cy3_outline.txt
│  │  │  ├─ ....