Dataset for the manuscript "Longitudinal spatial neutrophil profiling during ACT in murine melanoma reveals distinct lymph node infiltration patterns"

Dataset and code repository for the manuscript ["Longitudinal spatial neutrophil profiling during ACT in murine melanoma reveals distinct lymph node infiltration patterns"](https://doi.org/10.64898/2026.02.24.707484), which explores neutrophil and CD8 T cell kinetics and spatial organisation in tumor-draining vs non-draining lymph nodes in murine melanoma under adoptive T cell therapy. The manuscript is available as a preprint on [Bioarxiv](https://doi.org/10.64898/2026.02.24.707484). # Data repository act_neutrophil_data_repository├── figures│ ├── codex│ │ ├── manuscipt_plots│ │ ├── overview_intensity_images│ │ ├── patch_visualisations│ │ ├── phenotyping│ │ ├── spatial_analysis│ │ └── whole_LN_visualisations│ ├── flow_codex_comparison│ ├── flow_cytometry│ │ ├── lymph_node_sizes_all_conditions│ │ ├── main_conditions│ │ ├── no_cpg_conditions│ │ └── preprocessing│ ├── hematology│ └── tumor_growth_curves│ ├── merged│ ├── per_condition│ └── revision├── overview_of_experiments├── processed│ ├── codex│ │ ├── overview_intensity_images│ │ ├── revision│ │ └── statistics│ ├── flow_cytometry│ │ └── statistics│ ├── hematology│ │ └── statistics│ └── tumor_growth│ ├── metadata│ ├── per_experiment│ └── per_treatment└── raw ├── codex │ ├── data.... (folder per image) ├── flow_cytometry │ ├── cd8_panel │ ├── cd8_panel_prism_export │ ├── early_gates │ ├── pan_immune │ └── pmels_in_blood ├── hematology │ └── per_experiment └── tumor_growth└── Readme.md #ACT_melanoma_neutrophil code repository## General structure:- Scripts are sorted by data modality- Per modality, scripts are numbered by the order they should be executed in: - raw --> processed (script 0) - processed data files can be found in the data repository under 'processed' - processed --> postprocessing/analysis (script 1..n) - postprocessed/analysed files ready for the visualisation scripts can be found in the data repository under 'processed' - postprocessing/analysis --> visualisation for manuscript figures (script n+1). - figures as .pdf files can be found in the data repository under 'figures'- If two scripts/folders have the same number with a different letter (e.g. 2a, 2b), they can be executed in any order. If none of the scripts in a folder have a number, they can be executed in any order.- Where applicable, the (sub)figure number in the manuscript has been appended to the file name.## Running the code- Use either uv sync (preferred) or pip install -r requirements.txt- In `helper_files/paths_parameters`, update `data_repo_path` to the saved location of the data repository- Then you can start rerunning from anywhere, the data repository has all intermediate files saved. Per analysis, we recommend running it in the numbered order from preprocessing --> analysis --> visualisation.