npm - @brainpilot/skills - Versions diffs - 0.0.6 → 0.0.7 - Mend

@brainpilot/skills 0.0.6 → 0.0.7

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package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/report_template_en.html ADDED Viewed

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+<!DOCTYPE html>
+<html lang="en">
+<head>
+  <meta charset="UTF-8" />
+  <title>{{ report_title }}</title>
+  <style>
+    :root {
+      --page-width: 1100px;
+      --border: #d7dee7;
+      --ink: #1f1f1f;
+      --muted: #56697d;
+      --panel: #f5f8fb;
+      --accent: #1b4f72;
+    }
+    body {
+      font-family: "Noto Serif", Georgia, serif;
+      line-height: 1.7;
+      color: var(--ink);
+      margin: 0;
+      background: #eef3f7;
+    }
+    .page {
+      max-width: var(--page-width);
+      margin: 32px auto;
+      background: #ffffff;
+      padding: 40px 48px 56px;
+      box-shadow: 0 16px 40px rgba(22, 37, 56, 0.08);
+    }
+    h1, h2, h3 {
+      color: var(--accent);
+      line-height: 1.3;
+    }
+    h1 {
+      font-size: 28px;
+      margin: 0 0 20px;
+    }
+    h2 {
+      font-size: 22px;
+      margin: 36px 0 14px;
+      padding-bottom: 6px;
+      border-bottom: 1px solid var(--border);
+    }
+    h3 {
+      font-size: 18px;
+      margin: 24px 0 10px;
+    }
+    p {
+      margin: 10px 0;
+    }
+    ul {
+      margin: 10px 0 14px 20px;
+      padding: 0;
+    }
+    li {
+      margin: 6px 0;
+    }
+    .meta {
+      padding: 14px 18px;
+      background: var(--panel);
+      border-left: 4px solid #5c89b0;
+      margin-bottom: 28px;
+    }
+    figure {
+      margin: 20px auto 28px;
+      padding: 14px;
+      border: 1px solid var(--border);
+      background: #fafcfe;
+      max-width: 980px;
+    }
+    img {
+      display: block;
+      width: auto;
+      max-width: min(100%, 960px);
+      max-height: 560px;
+      height: auto;
+      margin: 0 auto;
+      object-fit: contain;
+    }
+    figcaption {
+      margin-top: 10px;
+      text-align: center;
+      color: var(--muted);
+      font-size: 14px;
+    }
+    code {
+      background: #eef3f7;
+      padding: 1px 5px;
+      border-radius: 4px;
+      font-size: 0.95em;
+    }
+    a {
+      color: #18507a;
+      text-decoration: none;
+    }
+    a:hover {
+      text-decoration: underline;
+    }
+  </style>
+</head>
+<body>
+  <div class="page">
+    <h1>{{ report_title }}</h1>
+    <div class="meta">
+      <div><strong>Project Path:</strong> {{ project_path }}</div>
+      <div><strong>Report Mode:</strong> {{ report_mode }}</div>
+      <div><strong>Report Goal:</strong> {{ report_goal }}</div>
+    </div>
+    {{ body_html }}
+  </div>
+</body>
+</html>

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/report_template_en.md ADDED Viewed

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+# {{ report_title }}
+{{ project_summary_section }}
+{{ overview_section }}
+{{ sample_check_section }}
+{{ raw_trajectory_section }}
+{{ heatmap_section }}
+{{ radar_section }}
+{{ stats_section }}
+{{ cluster_section }}
+{{ single_subject_section }}
+{{ integrated_interpretation_section }}

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/cluster-section.md ADDED Viewed

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+## Clustering Results
+{{ cluster_body }}
+{{ cluster_gallery }}

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/heatmap-section.md ADDED Viewed

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+## Heatmap and Trajectory Results
+{{ heatmap_body }}
+{{ heatmap_gallery }}

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/integrated-interpretation.md ADDED Viewed

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+## Integrated Interpretation
+{{ integrated_interpretation_body }}

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/overview.md ADDED Viewed

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+## Project Overview
+{{ overview_body }}

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/project-summary.md ADDED Viewed

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+## Project Overview and Materials
+{{ project_summary_body }}

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/radar-section.md ADDED Viewed

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+## Radar Plot Results
+{{ radar_body }}
+{{ radar_gallery }}

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/raw-trajectory.md ADDED Viewed

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+## Raw Trajectory Summary
+{{ raw_trajectory_body }}

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/sample-check.md ADDED Viewed

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+## Sample and Group Verification
+{{ sample_check_body }}

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/single-subject-section.md ADDED Viewed

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+## Single-Subject Results Overview
+{{ single_subject_body }}

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/stats-section.md ADDED Viewed

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+## Statistical Summary Plot Results
+{{ stats_body }}
+{{ stats_gallery }}

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/experiment-types/epm.md ADDED Viewed

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+# EPM
+`EPM` stands for Elevated Plus Maze.
+## What It Primarily Evaluates
+- Open-arm exploration
+- Closed-arm preference
+- Time in center and transitions between arms
+- In some projects, also looks at the balance between exploration and avoidance combined with total activity
+## Common Experimental Procedure
+- Apparatus usually consists of two open arms and two closed arms
+- Animal starts exploring from the center
+- Record time in and entries to open arms, closed arms, and center within fixed duration
+## Common Readouts
+- Time in open arms
+- Open arm entries
+- Time in closed arms
+- Time in center
+- Total arm entries
+- Total distance
+## How to Write When Only Raw Skeleton Data Exists
+- First look at where trajectories are mainly concentrated, rather than saying "only have materials, cannot summarize"
+- If device orientation is not clearly labeled, prioritize writing distribution in "longitudinal axis / transverse axis / center", do not force naming open arms and closed arms
+- If grouping prefixes like `control`, `model` are already obvious, can directly compare which group has larger lateral spread, which group is more concentrated near center or axis
+- Can directly write "larger / more concentrated activity range", "more / fewer center transitions", "more biased toward certain axis activity"
+## How to Summarize in Reports
+- When formal area indicators exist, first summarize whether open-arm exploration increases or decreases, then see if total entries or total distance change synchronously
+- When only raw trajectories exist, first summarize which type of area activities are mainly concentrated in, then write whether activity range contracts or expands
+- In multi-sample projects, if differences between `control` and `model` are already intuitive, can directly write which group is more dispersed, which is more concentrated
+- Single-sample projects can directly summarize trajectory features like "mainly active near center and certain axis", "limited lateral spread"
+## Recommended Summary Style
+- "Trajectories mainly concentrated on the longitudinal axis passing through center, with relatively limited lateral spread."
+- "`control` group has larger lateral activity range, `model` group trajectories more concentrated near center and axis areas."
+- "Overall sample has larger activity range, with frequent transitions between center and arm sections."
+- "If combined with formal area statistics, open-arm exploration is reduced, overall more biased toward closed areas."
+## Do Not Overstep
+- Do not directly write reduced open-arm exploration as clinical anxiety diagnosis
+- Do not ignore motor ability confounds from decreased total entries or total activity
+- Only have axis distribution, no device mapping: do not force longitudinal and transverse axes as confirmed open/closed arms

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/experiment-types/fst.md ADDED Viewed

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+# FST
+`FST` stands for Forced Swim Test.
+## What It Primarily Evaluates
+- Behavioral responses to inescapable water environment stress
+- Commonly used for antidepressant-like efficacy screening
+## Common Experimental Procedure
+- Place the animal in a water tank or cylindrical container from which it cannot escape
+- Record swimming, struggling, and immobility within a fixed duration
+- Some protocols include pre-test and test session
+## Common Readouts
+- Immobility time
+- Latency to immobility
+- Swimming time
+- Climbing / struggling time
+## How to Summarize in Reports
+- Directly summarize the main change direction of immobility time, swimming time, or struggling time
+- If behavioral typing is clear, can directly write "increased passive coping / increased active coping"
+- Single-sample projects can directly summarize the main coping style
+## Recommended Summary Style
+- "Increased immobility time, showing more obvious passive coping."
+- "More swimming and struggling time, overall showing more active stress coping."
+## Do Not Overstep
+- Do not write FST alone as sufficient evidence for "enhanced/reduced depression-like behavior"
+- Do not ignore protocol differences, such as whether there is a pre-test

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/experiment-types/nor.md ADDED Viewed

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+# NOR
+`NOR` stands for Novel Object Recognition.
+## What It Primarily Evaluates
+- Recognition memory
+- Novelty preference
+## Common Experimental Procedure
+Usually includes two core phases:
+1. Familiarization / training phase: Animal is exposed to two identical or equivalent objects
+2. Test phase: Replace one of the objects with a novel object and record exploration preference
+## Common Readouts
+- Novel object exploration time
+- Familiar object exploration time
+- Discrimination index
+- Preference index
+- Total object exploration time
+## How to Summarize in Reports
+- First summarize whether preference for novel object increases, decreases, or is not obvious
+- If discrimination index or preference index exists, directly write the direction
+- Single-sample projects can directly summarize as "prefers novel object / prefers familiar object / preference not obvious"
+## Recommended Summary Style
+- "Longer exploration time for novel object, showing obvious novelty preference."
+- "Decreased novelty preference, with decreasing discrimination index."
+## Do Not Overstep
+- Do not write NOR alone as "comprehensive learning memory impairment/recovery"
+- Do not ignore object attraction differences and side bias

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/experiment-types/oft.md ADDED Viewed

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+# OFT
+`OFT` stands for Open Field Test.
+## What It Primarily Evaluates
+- Spontaneous locomotor activity
+- Novelty-driven exploration
+- Partial indicators of anxiety-like behavior, such as center avoidance or thigmotaxis
+## Common Experimental Procedure
+- Place the animal in an open field (square or circular arena)
+- Record movement trajectory and behavior within a fixed duration
+- Often divide the arena into center zone and periphery
+## Common Readouts
+- Total distance traveled
+- Average velocity
+- Time in center
+- Center entries
+- Thigmotaxis (wall-hugging behavior)
+- Rearing
+- Immobility
+## How to Summarize in Reports
+- First summarize whether activity increases, decreases, or remains stable
+- Then summarize whether center exploration and periphery preference change
+- If total distance and center exploration direction are consistent, can directly write conclusions like "decreased activity accompanied by reduced center exploration"
+- Single-sample projects can directly summarize as "high/low activity", "more/less center exploration", "obvious/not obvious thigmotaxis"
+## Recommended Summary Style
+- "Decreased locomotor activity, accompanied by reduced center exploration."
+- "Test animals stay more in the periphery, showing obvious thigmotaxis."
+- "Increased center entries suggests enhanced center exploration in the open field."
+## Do Not Overstep
+- Do not directly write changes in center time as changes in anxiety level while completely ignoring activity level
+- Do not write OFT alone as depression-like conclusions

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/experiment-types/tcst.md ADDED Viewed

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+# TCST
+`TCST` in this skill refers to Three-Chamber Social Test (Three-Chamber Sociability and Social Novelty Test).
+## What It Primarily Evaluates
+- Sociability
+- Social novelty preference
+- In some designs, can also reflect social recognition
+## Common Experimental Procedure
+Typical procedure is divided into 2 to 3 phases:
+1. Habituation phase: Subject mouse freely explores the three-chamber apparatus
+2. Sociability phase: Stranger mouse placed on one side, empty cup/cage on the other side
+3. Social novelty phase: Familiar mouse on one side, novel stranger on the other side
+## Common Readouts
+- Time in each chamber
+- Time near stimulus cup/cage
+- Sniffing time
+- Entries to each chamber
+- Social preference index
+- Social novelty index
+## How to Summarize in Reports
+- If data comes from "stranger vs empty cup" phase, prioritize summarizing whether sociability increases or decreases
+- If data comes from "familiar vs novel stranger" phase, prioritize summarizing whether social novelty preference exists
+- If only chamber time is available, can directly summarize spatial preference and social cue preference direction
+- Single-sample projects can directly write "this sample mainly stayed on which side, approached which type of stimulus more"
+## Recommended Summary Style
+- "In the sociability phase, the subject mouse spent more time in the chamber containing the stranger mouse, suggesting strong sociability."
+- "In the social novelty phase, the subject mouse approached the novel stranger more, showing social novelty preference."
+- "Current single-sample results show that this sample mainly stayed in... area and approached... stimulus more."
+## Do Not Overstep
+- Do not directly write chamber time differences as "impaired social memory" unless the design and indicators sufficiently support it
+- Do not automatically interpret low-activity samples as social avoidance
+- Do not write single TCST results as complete autism-like behavioral conclusions

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/experiment-types/tst.md ADDED Viewed

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+# TST
+`TST` stands for Tail Suspension Test.
+## What It Primarily Evaluates
+- Behavioral responses to inescapable stress
+- Commonly used for antidepressant-like efficacy screening
+## Common Experimental Procedure
+- Mice are suspended by fixing their tails
+- Record struggling and immobility within a fixed duration
+- Common duration is 6 minutes
+## Common Readouts
+- Immobility time
+- Latency to immobility
+- Mobility / struggling time
+## How to Summarize in Reports
+- Directly summarize whether immobility time increases or decreases
+- If latency or struggling time exists, also directly write the direction of active coping or passive coping
+- Single-sample projects can summarize as "mainly immobile" or "more struggling"
+## Recommended Summary Style
+- "Increased immobility time suggests enhanced passive coping."
+- "Decreased immobility time, with increased struggling time, indicates more active stress coping."
+## Do Not Overstep
+- Do not directly write TST results as "having depression" or "higher depression level"
+- Do not ignore the effects of motor ability or sedative effects on immobility

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/input-types.md ADDED Viewed

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+# Input Types
+Read this file when determining "what materials are available in the project path for generating reports".
+## Common Input Types
+### Raw or Semi-Raw Data
+- `.h5`: Common for skeleton, trajectory, keypoints, or intermediate results.
+- `.csv` / `.xlsx`: Common for behavioral summary tables, event tables, significance test results.
+- `txt` / `yaml` / `json`: Common for parameter orders, group name descriptions, configuration files.
+These files are typically used to determine:
+- Whether there is single-sample or multi-sample data.
+- Whether group labels exist.
+- Whether there are quantifiable tables that can support figure interpretation.
+### Image or Document Results
+- Heatmaps, trajectory plots: spatial distribution, activity paths, velocity distributions.
+- Radar plots: multi-parameter profiles, group mean comparisons, single-sample overviews.
+- Violin plots / box plots: parameter distributions and inter-group differences.
+- Cluster plots / clustermap: sample or parameter pattern structures.
+These files are typically used for:
+- Generating figure captions.
+- Organizing result sections.
+- Deciding which figures go into the main text and which are suitable for appendices.
+## Priority Questions When Scanning Within Path
+1. Are there file names or table columns that can identify samples.
+2. Are there group labels, but do not automatically interpret label meanings.
+3. Are there statistical result tables like `stats_overall.csv`, `stats_pairwise.csv`.
+4. Are there figures representing overall patterns, such as group means radar, clustermap.
+5. Are there same-directory description texts, experimental notes, or background information supplemented by the user in conversation.
+## Handling Principles When Materials Are Incomplete
+- Only figures, no tables: Can do figure organization and conservative descriptions, do not make strong statistical interpretations.
+- Have tables, no figures: Can generate text-based result summaries, but image display is limited.
+- Have multiple figure types but no background: First do material inventory and ask the user questions.
+- Only single sample: Prioritize switching to `single-subject` mode.
+## Minimum Judgment Items to Output to Upper Flow
+At least judge and organize these boolean or summary fields:
+- `has_skeleton_data`
+- `has_behavior_summary`
+- `has_stats_tables`
+- `has_heatmaps`
+- `has_radar`
+- `has_cluster_figure`
+- `sample_count_detected`
+- `group_labels_detected`
+- `metadata_files_found`

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/interpretation-guardrails.md ADDED Viewed

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+# Interpretation Guardrails
+Read this file when generating result interpretation and summary text.
+## General Principles
+- First give the most direct result conclusions, then add a sentence about which figures or tables they are based on.
+- Prioritize summarizing "the most obvious characteristics of current data", do not give up normal summarization just because background is incomplete.
+- Separate "observed facts" from "interpretations based on experimental paradigm", but do not repeat limitation statements in every paragraph.
+- If key limitations truly exist, concentrate them in one section briefly, do not repeatedly write disclaimers throughout.
+## Allowed Conclusion Types to Write Directly
+- Main activity areas, preference directions, entry patterns, residence patterns of single samples
+- High/low differences already clearly presented between multiple groups in images or statistical tables
+- Simple summaries based on trajectory axis distribution, activity range, and path length when only raw skeleton data exists
+- Readout conclusions directly corresponding to experimental paradigm, e.g., increased open-arm exploration, decreased center exploration, enhanced novel object preference
+## Not Allowed to Overstep Situations
+- When only ambiguous abbreviation labels exist, do not explain inter-group relationships
+- When no statistical tables exist, do not write "significantly increased / significantly decreased"
+- Cluster plot showing separation does not equal statistical significant difference
+- Heatmap showing activity distribution does not equal mechanistic conclusions
+- Single-sample results should not be written as group-level patterns
+- Obvious file name prefixes like `control`, `model`, `sham`, `vehicle` can be used as candidate groupings first; other abbreviations should not be directly interpreted as biological groupings
+## Recommended Expression Style
+- "Results show..."
+- "Images and statistical results together indicate..."
+- "This sample mainly exhibits..."
+- "Under this experimental paradigm, this typically corresponds to..."
+- "If looking only at evidence within the current project path, the most obvious characteristic is..."
+## Conclusion Levels
+Prioritize output with the following strength:
+1. Direct result summary
+2. Comparisons with statistical support
+3. Interpretations combined with experimental paradigm
+4. Mechanistic conclusions
+Default should cover levels 1 to 3. Only enter level 4 when user explicitly allows and evidence is sufficient.

package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/metadata-schema.md ADDED Viewed

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+# Metadata Schema
+Read this file when determining "what information must be confirmed with the user".
+## Key Metadata
+The following information, if cannot be confirmed from the project directory, file names, figure titles, or user conversation, should first be asked to the user:
+- `project_name`: Project name or report title
+- `report_goal`: Report purpose, e.g., result organization, internal reporting, manuscript draft
+- `experiment_type`: Experimental paradigm or task type
+- `has_groups`: Whether groupings exist
+- `group_mapping`: What each group label represents
+- `control_group`: If there is a control group, which group is the control
+- `allow_interpretive_conclusion`: Whether interpretive conclusions are allowed
+## Recommended Supplementary Information
+- `species`
+- `sample_definition`: Whether one record corresponds to individual, session, trial, or other unit
+- `preferred_language`
+- `priority_figures`
+- `main_result_dirs`
+- `notes`
+## Where This Information Comes From
+There are only three sources of metadata:
+- Existing description texts, result files, and figure titles within the project directory
+- Information that can be directly inferred from file names, directory names, and sample naming conventions
+- Experimental background and writing requirements supplemented by the user in conversation
+## Questioning Rules
+- Missing `project_path`: Ask for the path first, do not do other work
+- When group names are obvious labels like `control`, `model`, `sham`, `vehicle`, they can be used as candidate groupings first
+- When group names are opaque abbreviations like `Y`, `con`, `k`, ask for group meaning first
+- Need to write formal inter-group comparisons but no `control_group`: Ask for control group first
+- User requests interpretive conclusions but `allow_interpretive_conclusion` is unclear: Ask if allowed
+## What Can Be Written When Unconfirmed
+Even if metadata is incomplete, the following are allowed to be output first:
+- Project and material overview
+- Sample and candidate grouping verification
+- Raw trajectory summary
+- Direct summary of image and statistical results
+Do not avoid obvious data characteristics just because of a small amount of missing background; only when key information is truly missing, do not hard-interpret opaque abbreviations as formal experimental group definitions.
+## Relationship with Manifest
+- `build_report_manifest.py` will aggregate unconfirmed items into `facts.unconfirmed_items`
+- When agents fill in `project_summary_body`, `overview_body`, `sample_check_body`, they can briefly mention key points that still need confirmation
+- All body text is directly filled back into `manifest.json`, no additional configuration or section files are created