All tools use the @tool decorator and are auto-registered on import.
Source: gently/agent/tools/ (run mode) and gently/agent/plan_mode/tools/ (plan mode).
| Tool | Description |
|---|
acquire_volume | Acquire a single 3D lightsheet volume for a specific embryo with calibration data |
capture_lightsheet | Capture a single 2D lightsheet fluorescence image at specified piezo/galvo position |
batch_lightsheet | Capture lightsheet images from ALL embryos and show them in the web UI viewer |
| Tool | Description |
|---|
analyze_volume | Analyze embryo volume using Claude Vision API |
get_detection_summary | Get summary of all detections across all embryos |
| Tool | Description |
|---|
calibrate_embryo | Run full piezo-galvo calibration for a specific embryo using Claude vision |
calibrate_all_embryos | Run piezo-galvo calibration for all detected embryos sequentially |
| Tool | Description |
|---|
detect_embryos | Automatically detect embryos using brightness detection and SAM segmentation |
manual_mark_embryos | Open interactive window to manually mark embryos by clicking |
edit_embryos | Add/remove/move embryo positions in the web map view |
show_detected_embryos | Capture fresh image and display all tracked embryos with labeled bounding boxes |
| Tool | Description |
|---|
list_detectors | List all registered detectors and their status |
enable_disable_detector | Enable or disable a specific detector |
remove_detector | Remove a detector from the registry |
add_detector | Add a new detector with custom detection prompt |
enable_preset_detector | Enable a preset detector (hatching, comma, pretzel, gastrulation, first_division) |
generate_detector_prompt | Generate optimal detection prompt from a description |
test_detector | Test a detector on a specific embryo's latest image |
query_timeline_events | Query timeline for detection and timelapse events |
| Tool | Description |
|---|
get_experiment_summary | Get comprehensive summary of current experiment |
query_embryo_status | Query detailed status of a specific embryo |
skip_embryo | Mark embryo to skip in future acquisitions |
remove_embryo | Permanently remove embryo from experiment |
resume_embryo | Resume imaging a previously skipped embryo |
assign_nickname | Assign memorable nickname to an embryo |
modify_parameters | Modify acquisition parameters for an embryo |
| Tool | Description |
|---|
fine_focus | Perform fine focus adjustment by scanning piezo positions and finding optimal focus |
get_focus_score | Calculate focus score for the current lightsheet image without moving the piezo |
get_focus_history | Get focus history for an embryo showing all piezo-galvo measurements over time |
| Tool | Description |
|---|
ask_user_choice | Present user with selectable options for discrete choices |
| Tool | Description |
|---|
set_led | Set the LED illumination state |
get_led_status | Get current LED illumination status |
| Tool | Description |
|---|
execute_plan_item | Execute a planned imaging item — resolve spec, configure parameters, start timelapse |
complete_current_plan_item | Mark the currently executing plan item as complete |
| Tool | Description |
|---|
assess_image_quality | Assess image quality metrics (focus, brightness, noise) and suggest adjustments |
get_session_stats | Get statistics for the current session (interactions, corrections, tool usage) |
compare_embryo_development | Compare developmental progress across multiple embryos |
analyze_corrections | Analyze user corrections from interaction logs to identify patterns |
export_interaction_log | Export interaction logs for external analysis |
import_embryos_from_session | Import embryos (positions, calibration, settings) from another session |
list_sessions | List available sessions with IDs, embryo counts, and last active times |
| Tool | Description |
|---|
move_to_embryo | Move XY stage to a specific embryo's stored position |
get_stage_position | Get current XY stage position in micrometers |
move_stage | Move XY stage to specific coordinates in micrometers |
| Tool | Description |
|---|
generate_bluesky_plan | Generate a Bluesky acquisition plan from a scientific goal |
start_adaptive_timelapse | Start an adaptive timelapse that runs in the background |
get_timelapse_status | Get current status of the running timelapse including per-embryo progress |
modify_timelapse_embryo | Modify parameters for a specific embryo during a running timelapse |
add_embryo_to_timelapse | Add an embryo to an already running timelapse |
stop_timelapse_embryo | Stop imaging a specific embryo (others continue) |
stop_timelapse | Stop the entire timelapse acquisition |
pause_timelapse | Pause the timelapse (can be resumed) |
resume_timelapse | Resume a paused timelapse |
add_stop_condition | Add an additional stop condition to a running timelapse (OR logic) |
add_interval_speedup_rule | Add rule to speed up imaging when a developmental stage is reached |
enable_pre_hatching_speedup | Enable automatic speedup when embryos approach hatching |
classify_embryo_stage | Use Claude Vision to classify the current developmental stage |
get_stage_history | Get the developmental stage progression history for an embryo |
predict_hatching | Predict time-to-hatching with confidence intervals based on stage |
| Tool | Description |
|---|
view_image | Capture and display current bottom camera widefield image |
view_volume | Open a volume in the in-browser 3D viewer |
list_volumes | List available volumes for an embryo or all embryos |
| Tool | Description |
|---|
create_campaign | Create a research campaign or phase (top-level research goal) |
create_plan_item | Create a plan item (imaging, bench, genetics, analysis, or decision_point) |
update_plan_item | Update fields on an existing plan item |
link_plan_items | Add a dependency between two plan items |
get_plan_item | Get full details of a plan item by ID |
propose_plan | Generate a complete experimental plan from a research goal |
get_plan_status | Get campaign status with phase breakdown and progress |
batch_update_status | Update status of multiple plan items at once |
batch_update_spec | Update imaging/bench spec fields for multiple items |
move_plan_item | Move a plan item to a different campaign or phase |
delete_plan_item | Delete a plan item |
reorder_plan_items | Reorder plan items within a campaign/phase |
update_phase | Update phase metadata (title, description, phase_number) |
delete_phase | Delete a phase and all its plan items |
export_plan | Export a campaign as structured YAML/JSON |
snapshot_plan | Create a named snapshot of the current plan state |
list_plan_versions | List saved plan snapshots for a campaign |
restore_plan_version | Restore a plan from a saved snapshot |
| Tool | Description |
|---|
query_lab_history | Search past sessions, campaigns, and learnings for relevant context |
check_hardware_capability | Check if the current hardware supports a requested capability |
| Tool | Description |
|---|
search_literature | Search scientific literature (PubMed) for relevant papers |
search_strains | Search strain/gene databases (WormBase, NCBI Gene) |
read_paper | Fetch and summarize a paper by DOI or PubMed ID |
| Tool | Description |
|---|
save_plan_template | Save the current campaign as a reusable template |
list_templates | List all saved plan templates |
apply_template | Create new campaign from a saved template with optional overrides |
| Tool | Description |
|---|
validate_plan | Validate a plan for errors and warnings (hardware limits, dependencies, completeness) |