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Image Table

Summary

The image table is a metadata table that tells PyFLASH where image files are, which subject and marker they belong to, and how to arrange ROI panels. It is stored on processed objects as .images. A nested lookup dictionary, .imagesDict, is rebuilt from the same table for quick subject/marker/ROI path lookup.

The table stores paths and labels, not the image pixels needed for long-term serialization.

Where It Appears

  • Experiment.images after Experiment.importImages() or Experiment.processData(import_images=True).
  • Batch.images after Batch.importImages() or Batch.processData(import_images=True).
  • Experiment.getImageTable(include_summary=True) and Batch.getImageTable(include_summary=True).
  • UI image helpers and image plot functions.

Required Fields

The base image table fields are:

Field Meaning
AnimalName Subject/sample folder name.
Marker Marker parsed from the image filename.
ROI ROI part parsed from the image filename. This can be blank when the filename has no ROI suffix.
ImageName Image file stem without extension.
ImagePath Local path to the image file.
Extension Lowercase file extension such as .png, .tif, or .jpg.

Batch image tables also include:

Field Meaning
Experiment Source experiment name before batch concatenation.

Optional Fields

When include_summary=True, PyFLASH attaches summary metadata by AnimalName:

Field Meaning
Condition Group label from the summary table.
Factor columns Columns such as Diagnosis, Sex, or Time from the group list.

Other image-related tables can include representative_images, a user-managed selection table for representative panels. That table is separate from .images but usually shares fields such as AnimalName, Marker, and ImageName.

Example

| Experiment | AnimalName | Condition | Marker | ROI | ImageName | ImagePath | Extension |
|---|---|---|---|---|---|---|---|
| Exp_01 | Mouse_01 | Control | GFAP | LHSCN | GFAP_LHSCN | /path/to/images/Mouse_01/GFAP_LHSCN.png | .png |
| Exp_01 | Mouse_01 | Control | DAPI | LHSCN | DAPI_LHSCN | /path/to/images/Mouse_01/DAPI_LHSCN.png | .png |

Nested lookup form:

image_path = batch.imagesDict["Mouse_01"]["GFAP"]["LHSCN"]

Produced By

  • Experiment.importImages(), which scans image folders under the experiment root.
  • Batch.importImages(), which concatenates experiment image tables and adds Experiment.
  • getImageTable(include_summary=True), which can refresh summary metadata.
  • UI helper functions that expose the object image table without importing Streamlit.

Consumed By

Notes

  • import_images=False leaves .images as None on processed objects and .imagesDict empty.
  • getImageTable(include_summary=False) returns only the base image metadata columns that exist on the table.
  • Image files are found by scanning known image folders. For current ImageJ-style exports, PyFLASH looks under Results/Presentation Images/Images and related analysis-image folders.
  • Image table sorting uses experiment, group, subject, ROI drawing order, marker, and image name when those fields are available.
  • Pickle serialization removes any ImageArray column if it exists, so rely on ImagePath for durable references.

See Also