Table 1.
List of files included in example dataset
| Folder | File | Description | Size | Step |
|---|---|---|---|---|
| SpinalJ_example_data_processed/ | Example dataset | 299 GB | n/a | |
| _Sample_Info.csv | Mouse genetics, staining and imaging info | 1 KB | n/a | |
| _Lost_Sections.csv | Sections lost during cryosectioning | 1 KB | 11 | |
| _PreProcessing_Parameters.csv | Parameters used for pre-processing | 1 KB | 14 | |
| _Cleaning_log.csv | User input during section clean up | 10 KB | 17 | |
| _II_Preview_Montage.tif | Down scaled single section images (reference channel montage) | 48.9 MB | 15 | |
| _IV_Preview_Montage_Clean.tif | Down scaled cleaned single section images (reference channel montage) | 43.5 MB | 17 | |
| _V_Preview_Montage_Aligned.tif | Down scaled, cleaned and aligned single section images (reference channel montage) | 341 MB | 18 | |
| SpinalJ_example_data_processed/_Output/ | Pre-processed image data, temporary files created during analysis, as well as resulting files | 38.5 GB | 19, 21 | |
| Analysis_Settings.csv | Parameters used for registration and analysis | 2 KB | 19 | |
| …/_Output/1_Reformatted_Sections/ | Single section images in rostro-caudal order, split by channel, and reference channel montage | 21.3 GB | 18 | |
| …/_Output/3_Registered_Sections/ | Registered single section images, split by channel | 8.7 GB | 21 | |
| …/_Output/4_Processed_Sections/ | Temporary processing data | 6.3 GB | 21 | |
| …/4_Processed_Sections/Detected_Cells/ | Cell detection data | 2 MB | 21 | |
| …4_Processed_Sections/Enhanced/ | Images enhanced for Ilastik pixel classification; split by channel | 4.1 GB | 20, 21 | |
| …/4_Processed_Sections/Measured_Intensities/ | Intensity data | 3 MB | 21 | |
| …/4_Processed_Sections/Object_Detection_Validation/ | Overlay of section images and detected cells; split by channel | 2.1 GB | 21 | |
| …/4_Processed_Sections/Probability_Masks/ | Probability masks created by Ilastik | 66 MB | 20, 21 | |
| …/4_Processed_Sections/Resampled_Cells/ | Cells mapped to atlas | 2 MB | 21 | |
| …/_Output/5_Analysis_Output/ | Analysis output | 2 GB | 21 | |
| Annotated_Volumes_XY_10_Z_25micron.csv | Volumes of atlas regions | 34 KB | 21 | |
| Transformed_Segment_Annotations.csv | Segment annotations transformed to match template length | 9 KB | 21 | |
| Template_Brain_Aligned.tif | Overlay of experimental SC data and SC template | 341 MB | 21 | |
| Transformed_Annotations.tif | Transformed atlas annotations | 341 MB | 21 | |
| Transformed_Hemisphere_Annotations.tif | Transformed hemisegment boundaries | 86 MB | 21 | |
| Transformed_Segments.tif | Transformed segment boundaries | 86 MB | 21 | |
| …/5_Analysis_Output/Cell_Analysis/ | Cell analysis output lists and graphs | 1.1 GB | 21 | |
| …/5_Analysis_Output/ Region_Mean_Intensity_Measurements_XY_10_Z_25micron/ | Intensity analysis output lists and graphs | 51 MB | 21 | |
| …./5_Analysis_Output/ Transform_Parameters/ | Transformation data | 9 MB | 21 | |
| …/_Output/Ilastik_Projects/ | Ilastik training file(s) | 255 MB | 20 c | |
| SpinalJ_example_data_raw 1-6 | Raw .nd2 images of block sections | 120 GB | 13 |