NeuroPilot Processing Analysis Report
PM240716085832027_d00029_2_soso_f5500_CellVideo_soso_f5500
RawNeuroPilot
Folder tag
PM240716085832027_d00029_02e2f319
Cell-type data
Yes
Dataset profile
neuronal
Representative frame
0
Imaging modality
2p
Colormap
black-to-green
Pixel size
0.645 um/pixel
Frame rate
10 Hz
Imaging modality: 2p (black-to-green colormap for intensity panels). Pixel size defaulted to 0.645 μm/pixel. Frame rate defaulted to 10.0 Hz.
Section A
A. Input Data Overview
A
Raw single frame / STD / MIP
Representative frame = 0; ROI box marks the crop shown below; black-to-green colormap
Source: D:\0_NurMar_shared_files\1_data\nanjing\Delive...so_f5500_CellVideo_soso_f5500\raw.tif
Shape
[5500,512,600]
dtype
uint16
fps
10 Hz
pixel size
0.645 μm/pixel
dynamic range
1.23e+03
bleaching drop %
0.048
SNR
15.8
motion mean px
55.4
Raw input quality is summarized with the representative single frame, STD, and MIP. The ROI box shows the crop location reused later in the comparison panel. Scale bars use the configured pixel size and all intensity displays follow the selected imaging modality colormap.
Section B
B. Integrated Improvement: Raw vs NeuroPilot
B
Raw vs NeuroPilot main grid (2x3)
Top row = Raw; bottom row = NeuroPilot; white ROI boxes mark the crop location
Source: D:\0_NurMar_shared_files\2_code\NeuroPilot_LLM...A1_test_live_v3\final\final_stack.tif
C
Matched ROI crop grid (2x3)
Crop coordinates = (237,262)-(307,332)
Source: D:\0_NurMar_shared_files\2_code\NeuroPilot_LLM...A1_test_live_v3\final\final_stack.tif
D
Kymograph group
NeuroPilot STD line map + Raw/NeuroPilot kymographs for line 1 and line 2
Source: D:\0_NurMar_shared_files\2_code\NeuroPilot_LLM...A1_test_live_v3\final\final_stack.tif
E
Raw vs NeuroPilot quantitative bars
SNR, motion mean, motion p95 and bleaching are shown as paired bars
Source: D:\0_NurMar_shared_files\2_code\NeuroPilot_LLM...\metrics\comparison_raw_vs_final.json
F
Motion curve
Frame-wise rigid motion magnitude converted to μm using the configured pixel size
Source: D:\0_NurMar_shared_files\2_code\NeuroPilot_LLM...\metrics\denoise\raw_rigid_shifts.npy
G
Correlation curve
frame-to-temporal-mean projection correlation
Source: D:\0_NurMar_shared_files\2_code\NeuroPilot_LLM...nal\integrated_correlation_curves.csv
The central comparison uses only Raw vs NeuroPilot, not intermediate denoise-only or registration-only displays. The same representative frame and deterministic crop are reused across all six images; quantitative differences are now shown as paired bar charts, while frame-wise rigid motion is plotted in μm and the correlation panel remains only in this integrated section.
Section C
C. Downstream Improvement
H
Raw segmentation map
Report display top percent = 60%; background = STD; labels = ROI rank
Source: D:\0_NurMar_shared_files\2_code\NeuroPilot_LLM...oi_selection\analysis_mask_uint16.tif
I
NeuroPilot segmentation map
Report display top percent = 60%; background = STD; labels = ROI rank
Source: D:\0_NurMar_shared_files\2_code\NeuroPilot_LLM...oi_selection\analysis_mask_uint16.tif
J
Downstream count comparison
Counts preserve analysis summary semantics
Source: D:\0_NurMar_shared_files\2_code\NeuroPilot_LLM...est_live_v3\segmentation\summary.json
K
Paired trace numbered map
Numbering matches trace panel
Source: D:\0_NurMar_shared_files\2_code\NeuroPilot_LLM...red_trace_anchor_labelmask_uint16.tif
L
Paired trace curves
Raw vs NeuroPilot traces on identical ROI anchors
Source: D:\0_NurMar_shared_files\2_code\NeuroPilot_LLM...aired_trace\paired_trace_summary.json
M
NeuroPilot cell correlation heatmap
All final analysis ROI shown; ROI order = final analysis rank ascending; value = Pearson correlation; colorbar = [-1, 1]
Source: D:\0_NurMar_shared_files\2_code\NeuroPilot_LLM...aired_trace\paired_trace_summary.json
N
NeuroPilot cell temporal heatmap
All final analysis ROI shown; ROI order = final analysis rank ascending; x-axis labels = time in seconds; colormap = RdBu_r; bin count = min(1000, frames); value = per-cell Z-score after binning; cells are rendered with square heatmap elements
Source: D:\0_NurMar_shared_files\2_code\NeuroPilot_LLM...aired_trace\paired_trace_summary.json
raw plane0 total
9211
NeuroPilot plane0 total
2494
raw accepted ROI
42
NeuroPilot accepted ROI
510
raw display selected
5
NeuroPilot display selected
51
paired trace displayed count
5
heatmap ROI count
510
Downstream visualization keeps the analysis counts unchanged while using a larger deterministic report-only subset for segmentation overview on STD backgrounds with ROI-rank labels. Paired traces remain a compact top-ROI view, while the correlation and temporal heatmaps now show the full final analysis ROI set in rank order, with the temporal axis labeled in seconds and the temporal heatmap rendered with square cells.
Section D
D. Provenance / Reproducibility
folder tag
PM240716085832027_d00029_02e2f319
pipeline LLM mode
apply
advisor backend
live
final_stack semantic
last_iter_denoised_output
raw stack path
D:\0_NurMar_shared_files\1_data\nanjing\Deliver_unus...9_2_soso_f5500_CellVideo_soso_f5500\raw.tif
final stack path
D:\0_NurMar_shared_files\2_code\NeuroPilot_LLM\tmp_p...rics\CA1_test_live_v3\final\final_stack.tif
iter params
[{"iter_index": 0,"effective_params": {"sample_mode"...tch_size": 6},"param_source": "llm_apply"}]
missing summary
none
This section records the frozen final_stack semantic, effective iteration parameters, and key artifact provenance consumed by the deterministic report builder.