AcqImage Metadata¶
CloudScope stores metadata with each AcqImage so GUI workflows and scripted workflows can use the same acquisition context.
Metadata is saved in the JSON sidecar next to the source image file.
For a source file named my_file.tif, CloudScope saves:
my_file.tif.json
The JSON sidecar stores image header metadata, user-editable experimental metadata, ROIs, and analysis summaries.
Experimental metadata¶
Experimental metadata is user-editable. These fields describe the biological sample, experimental condition, and notes associated with the image.
Experiment Metadata¶
| name | display_name | type | default | unit | choices | editable | group | description |
|---|---|---|---|---|---|---|---|---|
| species | Species | str | True | Animal | Animal species (e.g., mouse, rat). | |||
| sex | Sex | str | True | Animal | Biological sex or experimental sex label. | |||
| genotype | Genotype | str | True | Animal | Genotype or strain label. | |||
| region | Region | str | True | Sample | Brain region or anatomical location. | |||
| cell_type | Cell type | str | True | Sample | Type of cell or vessel being imaged. | |||
| depth | Depth | float | nan | True | Sample | Imaging depth in micrometers. | ||
| branch_order | Branch order | int | nan | True | Sample | Branch order for vascular structures. | ||
| direction | Direction | str | True | Sample | Flow direction or vessel orientation. | |||
| condition | Condition | str | True | Experiment | Experimental condition or treatment. | |||
| condition2 | Condition 2 | str | True | Experiment | Second condition field. | |||
| treatment | Treatment | str | True | Experiment | Treatment applied. | |||
| treatment2 | Treatment 2 | str | True | Experiment | Second treatment field. | |||
| date | Date | str | True | Experiment | User-editable date (e.g., experiment date). | |||
| note | Note | str | True | Notes | Free-form notes or comments. |
Image header metadata¶
Image header metadata is read from the source image file when available. Some calibration fields may be editable when users need to correct or provide missing physical units.
Image Header Metadata¶
| name | display_name | type | default | unit | choices | editable | group | description |
|---|---|---|---|---|---|---|---|---|
| shape | Shape | str | False | Header | ||||
| dims | Dims | str | False | Header | ||||
| sizes | Sizes | str | False | Header | ||||
| dtype | DType | str | False | Header | ||||
| num_channels | Channels | int | 0 | False | Header | |||
| num_scenes | Scenes | int | 0 | False | Header | |||
| date | Date | str | False | Header | ||||
| time | Time | str | False | Header | ||||
| physical_unit_y | Physical Unit Y | float | 1.0 | True | Calibration | |||
| physical_unit_x | Physical Unit X | float | 1.0 | True | Calibration | |||
| physical_label_y | Physical Label Y | str | Pixels | True | Calibration | |||
| physical_label_x | Physical Label X | str | Pixels | True | Calibration |