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4.6. Directory Organization

4.6.1. Directory Subfolders

The following folders are located in the <Dpath>\<Dname> folder and are intialized by the code for the AstroPath Pipeline. The most interesting folders for typical users are the upkeep_and_progress and the tmp_inform_data folders.

  1. upkeep_and_progress
    • For any upkeep and progress tracking files
    • Location of the AstropathAPIDdef_PP.csv files, where PP indicates the numeric project id
  2. flatfield
    • Location of the flatfield parameter files
    • These files are named Flatfield_BatchID_BB.bin, replacing the BB for the appropriate batch id.
  3. logfiles
    • Project level log files for the astropath pipeline
  4. Batch
    • The batch and merge tables
    • These tables are described in further documentation located here and here respectively
  5. Clinical
    • Location of the clinical table
    • These tables should be labeled as Clinical_Table_Specimen_XX_MMDDYYYY.csv, where the XX indicates the number on the <Dname> folder.
    • We always use the clinical table with the most recent date in the data upload
  6. Ctrl
    • Location of control TMA data output
  7. dbload
    • Location of the files used for the database upload
  8. tmp_inform_data
    • Location of the inform data output and inform algorithms used. Additional information on this folder is provided here
  9. reject
    • Location of the rejected slides

4.6.2. SlideID Subfolders

The following is the directory structure for each <SlideID> in the AstroPath Pipeline in the <Dpath>\<Dname> folders. The code initializes most of the folders if running the pipeline from the beginning and places data in the proper locations.

NOTE: <> indicate variables, lines without brackets indicate full names

+-- <Dname>\<Dpath> <br>
|  +-- <SlideID> <br>
|  |  +-- im3 <br>
|  |  |  +-- <ScanNN> <br>
|  |  |  |  +-- BatchID.txt <br>
|  |  |  |  +-- CheckSums.txt <br>
|  |  |  |  +-- <SlideID>\_<ScanNN>.annotations.polygons.xml <br>
|  |  |  |  +-- <SlideID>\_<ScanNN>\_annotations.xml <br>
|  |  |  |  +-- <SlideID>\_<ScanNN>\_annotations.xml.lock <br>
|  |  |  |  +-- <SlideID>\_<ScanNN>.qptiff <br>
|  |  |  |  +-- MSI <br>
|  |  |  |  |  +-- <SlideID>_[XXXX,YYYY].im3 files <br>
|  |  |  +-- flatw <br>
|  |  |  |  +-- <SlideID>_[XXXX,YYYY].im3 files <br>
|  |  |  +-- xml <br>
|  |  |  |  +-- <SlideID>_[XXXX,YYYY].xml files<br>
|  |  |  |  +-- <SlideID>.Full.xml
|  |  |  |  +-- <SlideID>.Parameters.xml
|  |  |  +-- <SlideID>-mean.csv <br>
|  |  |  +-- <SlideID>-mean.flt <br>
|  |  +-- inform_data
|  |  |  +-- Component_Tiffs
|  |  |  |  +-- <SlideID>_[XXXX,YYYY]_component_data.tif files
|  |  |  |  +-- <SlideID>_[XXXX,YYYY]_component_data_w_seg.tif files
|  |  |  |  +-- Batch.log
|  |  |  |  +-- batch_procedure.ifp
|  |  |  +-- Phenotyped
|  |  |  |  +-- <ABX>
|  |  |  |  |  +-- <SlideID>_[XXXX,YYYY]_cell_seg_data.txt
|  |  |  |  |  +-- <SlideID>_[XXXX,YYYY]_cell_seg_summary_data.txt
|  |  |  |  |  +-- <SlideID>_[XXXX,YYYY]_binary_seg_maps.tif
|  |  |  |  |  +-- Batch.log
|  |  |  |  |  +-- batch_procedure.ifp
|  |  |  |  +-- Results
|  |  |  |  |  |  +-- Tables
|  |  |  |  |  |  |  +-- <SlideID>_[XXXX,YYYY]_cleaned_phenotype_table.csv
|  |  |  |  |  |  |  +-- MaSSlog.txt
|  |  |  |  |  |  +-- QA_QC *See QC documentation for files*
|  |  +-- logfiles
|  |  +-- dbload
|  |  +-- geom
|  |  |  +-- <SlideID>_[XXXX,YYYY]_cellGeomLoad.csv

*link to QC documentation