DOI: 10.5061/dryad.crjdfn3ck
title: Data from: A comprehensive suite for extracting neuron signals across multiple sessions in one-photon calcium imaging

description: The dataset consists of calcium imaging data utilized for developing and
 validating CaliAli, a specialized suite for extracting neural signals from
 one-photon calcium imaging sessions under free-moving conditions across
 multiple sessions. Key components of this dataset include: Simulation
 codes used to generate synthetic data for this study. Source data
 corresponding to each figure presented in the study. The raw calcium
 imaging dataset employed in the research.
description: Calcium imaging data was obtained with a miniaturized microscope
 with flexible light source input (T-scope V4, Physiotech Inc,  Japan).
 Data was processed following the steps described in the CaliAli online
 documentation: https://caliali-pv.github.io/CaliAli/
description: # Data from: A comprehensive suite for extracting neuron signals across
 multiple sessions in one-photon calcium imaging
 [https://doi.org/10.5061/dryad.crjdfn3ck](https://doi.org/10.5061/dryad.crjdfn3ck) The dataset consists of raw and processed calcium imaging data utilized for developing and validating CaliAli, a specialized suite for extracting neural signals from one-photon calcium imaging sessions under free-moving conditions across multiple sessions. ## Description of Data and File Structure The dataset is organized into the following categories: * **video simulations**: Scripts for generating video simulations. * **Raw calcium imaging videos**: Unprocessed imaging data. * **Source data**: Processed data supporting key analyses. * **Extended source data**: Large datasets not included in *Source_data.xlsx*. * **Extracted neuronal signals**: Processed neuronal activity data. * **Codes**: Codes to process video data. ## Video simulations Codes used to generate synthetic data for this study can be found in the `Generate simulated data.zip`, along with detailed instructions. ## Raw Imaging Data Raw calcium imaging videos for data produced in this study are included in `.h5` format. **Folder Structure:** | **File Name (.zip)** | **Description** | | ---------------------- | ---------------------------------------------------------------------------------- | | *1h\_CA1\_recording* | Fig S14. Tracking performance evaluation over short timescales. | | *DG\_PVD\_data* | Fig 8, S15. Dentate gyrus recordings spanning 99 days. | | *Focal\_plane\_change* | Fig S6, S9. Imaging sessions acquired at different focal planes. | | *Opto\_data\_30mins* | Fig 7b-d, S13. Simultaneous imaging and optogenetic stimulation (30 min sessions). | | *Opto\_data\_4weeks* | Fig 7e-g. Simultaneous imaging and optogenetic stimulation over 4 weeks. | ## Source Data Quantitative data used for generating figures and conducting statistical analyses are stored in the *Source_data.xlsx* file. This file contains multiple sheets, each corresponding to a specific figure in the manuscript. Data are organized as follows: | **Sheet Name** | **Description** | **Variables** | | -------------- | ---------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------- | | *Fig. 2e* | Comparison of tracking algorithms based on correlation and crispness. | Algorithm (categorical), Correlation, Crispness | | *Fig. 3a* | Effect of inter-session gap on tracking accuracy. | Inter-session gap (days), BV similarity score, Tracking accuracy (%) | | *Fig. 3d* | BV similarity score and F1-score for neuron tracking. | BV similarity score, F1-score (%) | | *Fig. 4b* | Spatial correlation of GCaMP vs tdTomato neuronal projections. | Correlation | | *Fig. 6d* | # of neurons extracted by CaliAli vs. independent session processing. | Neuron count (%) | | *Fig. 6e* | Place decoding error within sessions. | Decoding error (cm) | | *Fig. 6g* | Percentage of neurons tracked across sessions. | Neuron count (%) | | *Fig. 6h* | Place field correlation values. | Correlation | | *Fig. 6k* | Decoding error across conditions (all neurons). | Decoding error (cm) | | *Fig. 6l* | Decoding error across conditions (only tracked across all sessions). | Decoding error (cm) | | *Fig. 6m* | Decoding error across conditions (downsampled to 100 neurons). | Decoding error (cm) | | *Fig. 7e* | Opto-consistency in misaligned data. | Misalignment amplitude (µm), Opto-consistent neurons (%) | | *Fig. 7h* | Opto-consistency across 4 weeks. | Neuron tracking method (categorical), Opto-consistent neurons (%) | | *Fig. 8c* | Population vector distances of session pairs obtained across 99 days. | Population vector distance | | *Fig. S1b* | Percentage of non-rigid misalignment in relation to the cumulative misalignment detected. | Misalignment (%) | | *Fig. S1c* | Misalignment amplitude observed within a 4-day gap. | Misalignment amplitude (µm) | | *Fig. S1d* | Misalignment amplitudes across time. | Misalignment amplitude (µm), Session gap (days) | | *Fig. S3e* | Alignment scores performance using different projections. | Alignment score | | *Fig. S3f* | Registration error using different projections. | Registration errors (µm) | | *Fig. S5b* | BV erosion effect on neuron extraction. | BV erosion level (%), Tracking accuracy (%) | | *Fig. S6e* | Spatial correlation of aligned neuron projections under z-axis displacements. | Correlation | | *Fig. S6f* | Correlation of XY-shifts between different focal planes. | Reference focal plane (µm), +60 µm focal plane (µm) | | *Fig. S6g* | Inter-session misalignment prediction across different focal planes. | Misalignment amplitude (µm) | | *Fig. S8b* | Extraction precision from standard initialization (S1) vs. residual initialization (S2). | Precision | | *Fig. S8c* | Overall extraction performance of CNMF-E batch vs. # of batches processed. | Number of sessions (#), F1-score (%) | | *Fig. S10c* | Temporal similarities between components extracted at different focal shifts. | Neuron similarity score | | *Fig. S12d* | Simulated and observed misalignment amplitude. | Misalignment amplitude (µm) | | *Fig. S12g* | Clustering accuracy with UMAP in drifting conditions. | Clustering accuracy (%) | | *Fig. S13d* | Reconstruction of segmented imaging data (5-minute segments). | Similarity with ground truth neurons (%) | | *Fig. S13e* | Reconstruction of segmented imaging data (15-minute segments). | Similarity with ground truth neurons (%) | | *Fig. S14c* | Mahalanobis distance of each component relative to the distribution from individually processed sessions. | Mahalanobis distance (D) | | *Fig. S14h* | Percentage of neuropile classifications for CNMF-E and CaliAli. | Neuropile classifications (categorical variable) | | *Fig. S15b* | Population vector distances of session pairs obtained across 99 days (undetected neurons have 0 activity). | Population vector distance | | *Fig. S15c* | Session gap effect on PVD. | Session gap (days), PVD | | *Fig. S15d* | PVD in non-aligned data. | Misalignment amplitude (µm), PVD | ## Extended Source Data The following datasets are too large to be included in *Source_data.xlsx* and are provided as *.mat* files: #### Data\_4e.mat – Neuron Pair Distances Across Alignment Algorithms Utilizing Dual-Color Imaging as GT | **Column** | **Description** | | ------------ | ---------------------------------------------------------------------------------------------------- | | *Algorithm* | Motion correction method used. | | *Projection* | Type of projection applied (e.g., BV+Neurons, Neurons, BV, Filt. Mean). | | *m21 - m30* | Mouse identities. Each column contains distances of GT neuron pairs (µm) in the corresponding mouse. | #### Data\_6b-c.mat – Spatial Information Content of Place Cells | **Column** | **Description** | | ----------- | ------------------------------------------- | | *Activity* | Average dF/F per neuron. | | *Info* | Spatial information content. | | *Mouse\_id* | Mouse identifier (1-4). | | *Method* | 0 = Single session processing, 1 = CaliAli. | | *Context* | Session number (1–4). | The table *Standardized_Info_content* contains the same variables, but *Info* is expressed as SD above chance (defined by random permutation). #### Data\_6h.pxp – Cumulative Probability of Place Field Correlation This *IgorPro* file contains the cumulative probability distribution of place field correlation. The raw data used to generate this histogram is included in the source data file. #### Data\_7b-d.mat – Opto-Consistency Values for Neuron Tracking | **Column** | **Description** | | ------------------ | ---------------------------------------------------------------------------- | | *Opto-consistency* | 1 if the neuron consistently responds to light across sessions, 0 otherwise. | | *Hyperparameter* | Correlation threshold used for neuron matching. | | *Opto-threshold* | Defines opto(+) neurons based on light response. | | *Method* | Tracking approach used. | ## Neuron Extraction Data Neuron extraction results from calcium imaging are provided as `.mat` files. Each file contains a table including some or all of the following variables: * **a**: `[F×N double]` Spatial components of extracted neurons, with F frames and N neurons, representing spatial activity over time. * **c**: `[N×F double]` Denoised temporal components, showing neuronal activity patterns after denoising. * **cr**: `[N×F double]` Raw temporal components, similar to `c` but without denoising. * **d**: `[d1×d2]` Video dimensions, specified as height (`d1`) × width (`d2`) in pixels. * **Al**: `[d1×d2×3 uint8]` Footprint projections, showing ground truth (GT) data, aligned extractions, and raw extractions. * **m**: `[N×2 double]` Temporal similarity of extracted neurons to GT neurons, measured using cosine similarity. * **t**: `[100×5 table]` Performance scores across different temporal similarity thresholds. * **s**: F1 score computed at a temporal similarity threshold of `0.8`. ### Included Datasets: | **Dataset** | **Description** | | -------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | **Fig\_5m-p\_neuron\_data.mat** | Simulated calcium imaging data evaluating SNR effects across sessions. Neurons were extracted using **Single session processing** or **CaliAli (concatenated sessions)**, with high and low SNR neurons (defined by GT data) analyzed separately. The table contains four columns: **Single session–High, Single session–Low, CaliAli–High, and CaliAli–Low**. | | **Fig\_6\_neuron\_data.mat** | Place cell recordings. **Cell array BH** contains the behavioral data of mouse position, while **T** holds the extracted neuronal data. | | **Fig\_7b-d\_neuron\_data.mat** | Opto-tracking data. The **Opto\_imaging table** includes rows for hyperparameters and columns for different extraction methods. The **opt (cell array)** contains light stimulation timings. | | **Fig\_7f-h\_neuron\_data.mat** | Opto-tracking data over a **4-week period** using different methods. The **opt (cell array)** includes light stimulation timings. | | **Fig8\_neuron\_data.mat** | Neuronal activity extracted over **99 days** using different methods. Includes **dateObjects**, which records the timing of each session. | | **Fig\_S5\_neuron\_data.mat** | Simulated data evaluating tracking performance under varying blood vessel (BV) clarity. Columns represent **levels of BV erosion**, and rows represent **simulation replicates**. **TCA** contains neurons extracted using **CaliAli**, and **TPC** contains neurons extracted using **Optimal Extraction**. | | **FigS6\_S10\_neuron\_data.mat** | Simulated data evaluating tracking performance under **focal plane displacements**, with rows representing different **focal plane shifts** and columns corresponding to different **tracking methodologies**. | | **Fig\_S9\_neuron\_data.mat** | Simulated data where **neuronal spatial components varied across sessions**, with rows representing **simulation replicates** and columns corresponding to different **extraction methods**. | | **FigS12\_neuron\_data.mat** | Simulated data under different conditions: **Dense** (dense neuronal distribution), **Remapping** (active neurons change across sessions), **Ideal** (non-dense, non-remapping distribution), and **Drift** (neurons gradually drift across conditions). Rows represent **simulation replicates**, and columns correspond to different **extraction methods**. | ## Code/Software Code used to process these data sets are included in [GitHub](https://github.com/CaliAli-PV/CaliAli) and in the [Online Documentation of CaliAli](https://caliali-pv.github.io/CaliAli/latest)