Excel Workbooks¶

Summary¶

Excel workbooks are human-facing exports from a processed Batch. They are useful for sharing summary values, per-object IF measurements, behavior columns, and extra batch-summary columns with collaborators who do not use Python.

Each workbook is paired with a *_RegexFilters.txt report that records which include/exclude regex filters were applied and which columns or sheets were exported or skipped.

Created By¶

Method	Default workbook
`batch.export_all_excel(...)`	Delegates to `batch.export_excel(...)` and writes all enabled workbook families.
`batch.export_excel(...)`	Coordinates IF summary, IF extended, behavior, and extra-summary exports.
`batch.export_IF_summary_excel(...)`	`IF_Summary.xlsx`
`batch.export_extended_data_excel(...)`	`IF_Extended.xlsx`
`batch.export_behavior_summary_excel(...)`	`Behavior_Summary.xlsx`
`batch.export_extra_summary_excel(...)` / `batch.export_unregistered_summary_excel(...)`	`Extra_Summary.xlsx`

The Streamlit UI export page calls the same Batch.export_all_excel(...) method through the UI service layer.

Folder Layout¶

If save_path=None, relative export paths resolve below batch.export_path, which defaults to:

<batch-output>/Exports/

export_excel(...) writes IF workbooks into one subfolder per ROI base and writes behavior/extra-summary workbooks into the export root:

<batch-output>/Exports/
  scn/
    IF_Summary.xlsx
    IF_Summary_RegexFilters.txt
    IF_Extended.xlsx
    IF_Extended_RegexFilters.txt
  Behavior_Summary.xlsx
  Behavior_Summary_RegexFilters.txt
  Extra_Summary.xlsx
  Extra_Summary_RegexFilters.txt

An explicit absolute save_path is used as-is. A relative save_path is resolved inside batch.export_path.

Custom workbook stems can be supplied without .xlsx, for example if_summary_save_name="SCN_IF". If a supplied stem ends in .xlsx, PyFLASH strips the extension before appending .xlsx and _RegexFilters.txt.

File Contents¶

IF Summary¶

IF_Summary.xlsx contains:

Sheet	Contents
`Experimental Conditions`	Condition factor, condition name, and explanation.
`Data Summary`	Per-experiment marker/analysis overview and any recorded ImageJ macro details found in analysis-detail text files.
One sheet per mapped summary metric	Values split into condition columns, with a metric description written below the data.

Only columns covered by the IF summary name map are exported here.

IF Extended¶

IF_Extended.xlsx contains:

Sheet	Contents
`Conditions`	Condition table.
`Experiment <n>_<marker>` or `Experiment <n>_<marker> ROI` sheets	Per-object or ROI-level rows from each antibody table, including ID columns and mapped metric columns.

The extended export writes mapped raw metric columns from each experiment's Antibody data tables. Unmapped or regex-skipped columns are reported in the matching regex text file.

Behavior Summary¶

Behavior_Summary.xlsx contains:

Sheet	Contents
`Conditions`	Condition table.
One sheet per behavior metric in the behavior name map	Values split into condition columns, with a description below the data when available.

If no Behaviour table is present in batch.data, the method returns without creating an export folder.

Extra Summary¶

Extra_Summary.xlsx contains:

Sheet	Contents
`Experimental Conditions`	Condition table.
`Extra Columns`	Index of exported internal column names, display names, and sheet names.
One sheet per unregistered summary column	Values split by condition, or an `All` group when no condition split is available.

Registered IF summary columns are deliberately excluded from Extra_Summary and listed in the regex report.

How To Reuse¶

Export all default workbook families:

batch.export_all_excel()

Export to an explicit folder with custom names:

batch.export_all_excel(
    save_path="analysis-output/exports",
    if_summary_save_name="SCN_IF_Summary",
    if_extended_save_name="SCN_IF_Extended",
    behaviour_save_name="Behaviour",
    unregistered_summary_save_name="Other_Summary",
)

Read one exported sheet back into Python:

import pandas as pd

df = pd.read_excel(
    "analysis-output/exports/scn/IF_Summary.xlsx",
    sheet_name="Experimental Conditions",
)
print(df.head())

Inspect an export audit report:

from pathlib import Path

report = Path("analysis-output/exports/scn/IF_Summary_RegexFilters.txt")
print(report.read_text(encoding="utf-8"))

Notes¶

Excel sheet names are sanitized for Excel's forbidden characters and 31 character limit. Duplicate or truncated names get numeric suffixes.
Include/exclude filters match internal PyFLASH column names, not display labels.
IF summary and IF extended workbooks are written per ROI base when using export_excel(...).
batch.export_excel(...) with all output toggles disabled creates no export folder.
On Windows, an open workbook can lock the file and prevent overwriting it.