Molecular Devices ImageXpress HCS.ai

Expected Data Structure

The MD ImageXpress converter expects an acquisition directory containing an .mxprotocol file and one or more experiment subdirectories:

{protocol_name}_{date-time}/
├── {protocol_name}.mxprotocol
├── autofocus/
└── experiment{_mode}/
    ├── {acquisition_name}.jdce
    ├── image_metadata_1.csv
    ├── timepoint0/
    │   └── {protocol_name}_t0_C05_s0_w0_z0.tif
    └── timepoint1/
        ├── {protocol_name}_t1_C05_s0_w0_z0.tif
        ├── {protocol_name}_t1_C05_s0_w0_z1.tif
        └── ...

Flexible path input

You can point Path to either the acquisition directory ({protocol_name}_{date-time}/) or directly to the .mxprotocol file. The converter handles both.

Metadata

The converter parses two files inside the experiment directory:

• .jdce (JSON) — Experiment-level metadata: channel/wavelength configuration, pixel size, objective calibration, Z-stack parameters, and time schedule.
• .csv — Per-image records: well position (row, column), field of view index, wavelength, Z index, timepoint, stage positions, and the relative path to each TIFF file.

Channel colors are automatically assigned based on the excitation wavelength defined in the .jdce file.

Experiment Modes

The microscope can produce up to three experiment directories, each containing a different type of data:

Directory	Content
experiment	Standard or projection images
experiment_z_stack	Full Z-stack acquisitions
experiment_montage	Montaged / stitched images

By default, the converter prefers experiment_z_stack if present, otherwise falls back to experiment. Use the advanced options below to select a different mode.

Task Parameters

The MD ImageXpress init task extends the base acquisition parameters with MD-specific advanced options:

Field	Type	Default	Description
Path	str	required	Path to the acquisition directory or .mxprotocol file.
Plate Name	str or null	null	Custom plate name. Defaults to the directory name.
Acquisition Id	int	0	Acquisition identifier for multi-acquisition plates.
Advanced	MDAcquisitionOptions	{}	Advanced options (see below).

MD-Specific Advanced Options

In addition to the common advanced options, the MD converter adds:

Field	Type	Default	Description
Convert Only Projections	bool	false	Only convert projection images from the experiment directory, ignoring Z-stacks.
Convert Montages	bool	false	Convert montaged / stitched images from experiment_montage instead of individual FOVs.

Incompatible options

Convert Only Projections and Convert Montages cannot both be enabled when the montage data contains Z-stacks.

Multiple Acquisitions (same plate)

To combine multiple acquisitions into a single plate, use different Acquisition Id values while keeping the same Plate Name.