Deployment of endocytic machinery to periactive zones of nerve terminals is independent of active zone assembly and evoked release.
Paper
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The authors' code
Python · 361 lines · 15 KB · GPL-3.0
- import pandas as pd
- from pathlib import Path
- import os
- import glob
- import tifffile as tif
- import PAZ_Processing as paz
- import numpy as np
- import seaborn as sns
- import matplotlib.pyplot as plt
- from scipy.stats import kstest, kruskal, f_oneway as anova, ttest_ind as ttest, mannwhitneyu as mwu
- import scikit_posthocs as ph
- ''' Classes to aggregate across experiments the various types of PAZ analysis data, including:
- Mesh intensity/localization/colocalization data stored in [X}-ALLTHECELLS.csv files
- Radial profile data stored in [X]-ALLTHEPROFILES.csv files
- Centroid distribution data stored per [img name]-centroids.csv file in [experiment]_centroids folders'''
- # An obvious alternative to these relatively more complex/specific structures would be to simply have a dataframe with experiment as a column value...
- # Indeed this is easier. Maybe make a class but just subclass df?
- #root_folder = "Z:\\Current members\\DelSignore\\Coding_Projects\\Analyze_PAZ_Data\\TestData"
- #version_num = 214
- # glob to find all specific version of analysis folders across all experiments
- #target_dirs = [path for path in Path(root_folder).rglob(f"Analysis-V{version_num}*")]
- #experiment_labels = [dir.name.split("_")[1] for dir in target_dirs]
- #for dir in target_dirs:
- # print(dir)
- #for lab in experiment_labels:
- # print(lab)
- class DataAggregate:
- def __init__(self, datasets=None, data_path=None, version_num=None, file_name=None, *args, **kwargs):
- assert datasets or data_path, "Must provide either a dataset or path etc to construct DataAggregate"
- if(datasets == None):
- self.datasets = self.load_data(data_path, version_num, file_name)
- else:
- self.datasets = datasets
- def load_data(self, data_path, version_num, file_name):
- '''
- Load .csv datasets and store as dictionary with experiment number as keys
- Note: Tried using glob and Path.rglob to recursively search dirs but
- this was *very* slow bc of large number of subdirs.
- '''
- exp_dirs = glob.glob(data_path+"*/")
- analysis_dirs = glob.glob(os.path.join(data_path,"*", f"*V{version_num}*/"))
- exp_labels = [dir.split("_")[0] for dir in exp_dirs]
- datasets = {}
- for exp, exp_dir in zip(exp_labels, exp_dirs):
- datasets[exp] = pd.read_csv(os.path.join(exp_dir, file_name))
- return datasets
- def filter(self, filter_cols, filter_vals):
- ''' filter all experiments by indicated columns.
- filter_cols is a list of strings containing column label(s) eg ['AZ_count']
- filter_vals is a list of strings containing filter expressions eg ['>0']'''
- filtered = {}
- filter_strings = [f"['{filter_col}']{filter_val}" for filter_col, filter_val in zip(filter_cols, filter_vals)]
- for experiment in self.datasets:
- filter_expression = [f"(self.datasets['{experiment}']{filter_string})" for filter_string in filter_strings]
- filter_expression = " & ".join(filter_expression)
- bool_filter = eval(filter_expression)
- filtered[experiment] = self.datasets[experiment][bool_filter]
- return filtered
- def average_by_image(self):
- grouped = {}
- for experiment in self.datasets:
- grouped[experiment] = self.datasets[experiment].groupby(['Image']).mean()
- return grouped
- def aggregate_experiments(self):
- return pd.concat(self.datasets)
- class MeshData(DataAggregate):
- def __init__(self, datasets=None, data_path=None, version_num=None, file_name=None, *args, **kwargs):
- super().__init__(datasets, data_path, version_num, file_name, *args, **kwargs)
- def average_by_image(self):
- averaged = super().average_by_image()
- return MeshData(datasets = averaged)
- def filter(self, filter_cols, filter_vals):
- filtered = super().filter(filter_cols, filter_vals)
- return MeshData(datasets = filtered)
- class ProfileData(DataAggregate):
- def __init__(self, datasets=None, data_path=None, version_num=None, file_name=None, *args, **kwargs):
- super().__init__(datasets, data_path, version_num, file_name, *args, **kwargs)
- def average_by_image(self):
- averaged = super().average_by_image()
- return ProfileData(datasets = averaged)
- def filter(self, filter_cols, filter_vals):
- filtered = super().filter(filter_cols, filter_vals)
- return ProfileData(datasets = filtered)
- class CentroidData(DataAggregate):
- def __init__(self, datasets=None, data_path=None, version_num=None, file_name=None, *args, **kwargs):
- super().__init__(datasets, data_path, version_num, file_name, *args, **kwargs)
- def average_by_image(self):
- averaged = super().average_by_image()
- return ProfileData(datasets = averaged)
- def filter(self, filter_cols, filter_vals):
- filtered = super().filter(filter_cols, filter_vals)
- return ProfileData(datasets = filtered)
- def superplot_df(df, measurements):
- ''' Take an aggregated dataframe and organize specific measurements
- into 'superplot' fashion by channels and measurements
- Row indices are hierarchical - Experiment - image'''
- if type(measurements) is not type([]):
- measurements = [measurements]
- splits = [col.split("_") for col in df.columns.values]
- unique_channels = list(set([colsplit[1] for colsplit in splits if len(colsplit)>1]))
- retrieve_cols = [f'{measure}_{channel}' for measure in measurements for channel in unique_channels]
- # figure out how to handle PCCs. Maybe have those without channels (ie don't underscore)?
- superplot = df[[*retrieve_cols]]
- return superplot
- def aggregate_experiment_pixels(imgdir):
- '''
- Iterate through images in one experiment folder:
- Make mask and signed distance tranform
- Normalize pixel intensities per channel based on masked region
- create aggregated dataframe listing edm and channel intensities per pixel
- imdir - path of format [ExperimentLabel]_[c1-label]_[cn-label]...
- returns pd.DataFrame containing Experiment, Image, EDM, and normalized
- channel intensity columns for all pixels in all images
- '''
- if(imgdir[-1] != os.path.sep):
- imgdir += os.path.sep
- exp = (imgdir.split(os.path.sep)[-2]).split("_")[0]
- chans = (imgdir.split(os.path.sep)[-2]).split("_")[1:4]
- alldata=pd.DataFrame(columns = ["Experiment", "Image", "EDM"] + chans)
- imgs = glob.glob(os.path.join(imgdir, "*.tif"))
- for img in imgs:
- imgn = tif.imread(img)
- mask = paz.segment(imgn, 1)
- sdm = paz.sdt(mask)
- imgn_norm = paz.norm_by_mask(imgn, mask, 1)
- fg_norm = imgn_norm[mask>0]
- fg_edm = sdm[sdm>-1]
- fg_norm = fg_norm.reshape(-1, imgn_norm.shape[-1])
- fg_edm = fg_edm.flatten()
- imgdf = pd.DataFrame(fg_norm)
- imgdf = imgdf.set_axis(chans, axis=1)
- imgdf["EDM"] = fg_edm
- imgdf["Image"]=os.path.basename(img)
- alldata = pd.concat([alldata, imgdf])
- alldata["Experiment"] = exp
- return alldata
- def aggregate_all_pixels(rootpath):
- exp_dirs = glob.glob(rootpath+"*/")
- allexpdata = pd.DataFrame()
- for expdir in exp_dirs:
- print(expdir)
- tempdf = process_folder(expdir)
- allexpdata = pd.concat([allexpdata, tempdf])
- return allexpdata
- def aggregate_csvs(root_dir, version, file_name, verbose=False):
- '''
- Open csv file and reorganize into regualrly formatted DataFrame ready to aggregate
- '''
- if(root_dir[-1] != os.path.sep):
- root_dir += os.path.sep
- exp_dirs = glob.glob(root_dir+"*/")
- analysis_dirs = glob.glob(os.path.join(root_dir,"*", f"*V{version}*/"))
- alldata=pd.DataFrame(columns = ["Experiment"])
- for analysis_dir in analysis_dirs:
- file = os.path.join(analysis_dir, file_name)
- if os.path.exists(file):
- exp = (analysis_dir.split(os.path.sep)[-2]).split("_")[-1]
- df = pd.read_csv(file)
- df["Experiment"] = exp
- alldata = pd.concat([alldata, df])
- if verbose:
- print(f"Loaded {df.shape[0]} meshes from experiment {exp}")
- return alldata
- def subset_pairwiseData(df, usecols=None, dropchannels=None):
- '''
- Take a PAZ dataframe and return a subset of columns [usecols].
- Optional exclude channels in [dropchannels]
- '''
- if usecols:
- if type(usecols) is not type([]):
- usecols=[usecols]
- measure_cols = [col for col in df.columns.values if
- any([check in col for check in usecols])]
- else:
- measure_cols = df.columns.values
- measure_cols.remove("Experiment")
- measure_cols.remove("Image")
- # Start with Experiment and Image columns necessary for sorting later
- dfsub = df.loc[:, ["Experiment"]]
- dfsub[measure_cols] = df.loc[:, measure_cols]
- if dropchannels:
- if type(dropchannels) is not type([]):
- dropchannels=[dropchannels]
- drop_cols = [col for col in dfsub.columns.values if
- any([check in col for check in dropchannels])]
- dfsub = dfsub.drop(drop_cols, axis = 1)
- return dfsub
- def subset_data(df, usecols=None, dropchannels=None):
- '''
- Take a PAZ dataframe and return a subset of columns [usecols].
- Optional exclude channels in [dropchannels]
- '''
- if usecols:
- if type(usecols) is not type([]):
- usecols=[usecols]
- measure_cols = [col for col in df.columns.values if
- any([check in col for check in usecols])]
- else:
- measure_cols = df.columns.values
- measure_cols.remove("Experiment")
- measure_cols.remove("Image")
- # Start with Experiment and Image columns necessary for sorting later
- dfsub = df.loc[:, ["Experiment", "Image"]]
- dfsub[measure_cols] = df.loc[:, measure_cols]
- if dropchannels:
- if type(dropchannels) is not type([]):
- dropchannels=[dropchannels]
- drop_cols = [col for col in dfsub.columns.values if
- any([check in col for check in dropchannels])]
- dfsub = dfsub.drop(drop_cols, axis = 1)
- return dfsub
- def norm_data(df, norm_col=None, melt=True, keep_scale=False):
- '''
- Given dataframe of PAZ data, return normalized dataframe
- Normalization is per row, so if rows are meshes, normalization will be at level of mesh.
- Default behavior is to normalize each column with values against each other column.
- Optionally, can set norm_col to one column against which to normalize all other columns.
- '''
- if norm_col:
- measure_cols = [norm_col]
- else:
- measure_cols = df.columns
- measure_cols = measure_cols.drop(["Experiment", "Image"])
- norm = df.loc[:, ["Experiment", "Image"]]
- for num in measure_cols:
- for den in measure_cols:
- if num is not den:
- norm[f"{num}-{den}"]=df.loc[:, num]/df.loc[:, den]
- if melt:
- melted = norm.melt(id_vars = ["Experiment", "Image"])
- melted[['C1', 'C2']] = melted['variable'].str.split('-', expand=True)
- melted = melted.drop("variable", axis=1)
- return melted
- else:
- return norm
- def superplot(df, data_order=None, box=True):
- melt = df.melt(id_vars = ["Experiment", "Image"])
- ImgMean = melt.groupby(["Experiment", "Image", "variable"]).mean().reset_index()
- ExpMean = melt.groupby(["Experiment", "variable"]).mean().reset_index()
- sp = sns.swarmplot(data=ImgMean, x="variable", y="value", hue="Experiment", size=5, order=data_order, zorder=0)
- sns.swarmplot(x="variable", y="value", hue="Experiment", size=12, edgecolor="k", linewidth=2, data=ExpMean, order=data_order, zorder=0)
- if box:
- sns.boxplot(data=ImgMean, x="variable", y="value",
- order=data_order,
- showfliers=False,
- whis=0,
- boxprops={'facecolor':'None', 'linewidth':2.5, 'edgecolor':'k'},
- medianprops = {'linewidth':5, 'color':'k'},
- whiskerprops={'linewidth':0},
- ax=sp)
- sp.legend_.remove()
- plt.xticks(rotation=45)
- def superplot_norm(df, data_order=None):
- ImgMean = df.groupby(["Experiment", "Image", "C1"]).mean().reset_index()
- ExpMean = df.groupby(["Experiment", "C1"]).mean().reset_index()
- sp = sns.swarmplot(data=ImgMean, x="C1", y="value", hue="Experiment", size=5, order=data_order)
- ax = sns.swarmplot(data=ExpMean, x="C1", y="value", hue="Experiment", size=12, edgecolor="k", linewidth=2, order=data_order)
- sp.legend_.remove()
- plt.xticks(rotation=45)
- def compareGroups(df, verbose=True):
- ImgPost = df.melt()
- ImgPost = ImgPost.loc[-np.isnan(ImgPost.value), :]
- # Check whether outcomes are normally distributed
- ks = [kstest(df.loc[df[col]>-1, col], 'norm') for col in df]
- kpass = True if np.min(np.array(ks)[:,1])>0.05 else False
- test_name = "ANOVA" if kpass else "Kruskal-Wallis"
- posthoc = pd.DataFrame()
- if kpass:
- #Do anova if vars normally distributed
- test = anova(*[df.loc[-np.isnan(df[col]), col] for col in df])
- if test[1] < 0.05:
- # Do posthoc ttest if model is significant
- posthoc = ph.posthoc_ttest(ImgPost, group_col='variable', val_col='value', p_adjust='sidak')
- else:
- # Do KW test to test if medians different
- test = kruskal(*[df.loc[:, col] for col in df], nan_policy='omit')
- if test[1] < 0.05:
- # Do posthoc dunns if model is significant
- posthoc = ph.posthoc_dunn(ImgPost, group_col='variable', val_col='value', p_adjust='sidak')
- if verbose:
- print(f"Performed {test_name}: test statistic = {test[0]} p-value:{test[1]}")
- return {'test':test_name, 'result':test, 'posthoc':posthoc}
- def ttestl(df, verbose=True):
- '''Assess distributions of groups to compare. If normal, do ttest. If not, do MWU test.'''
- ImgPost = df.melt()
- ImgPost = ImgPost.loc[-np.isnan(ImgPost.value), :]
- # Check whether outcomes are normally distributed
- ks = [kstest(df.loc[df[col]>-1, col], 'norm') for col in df]
- kpass = True if np.min(np.array(ks)[:,1])>0.05 else False
- test_name = "ttest" if kpass else "Mann-Whitney"
- posthoc = pd.DataFrame()
- if kpass:
- #Do ttest if vars normally distributed
- test = ttest(*[df.loc[-np.isnan(df[col]), col] for col in df])
- else:
- # Do KW test to test if medians different
- test = kruskal(*[df.loc[:, col] for col in df], nan_policy='omit')
- if test[1] < 0.05:
- # Do posthoc dunns if model is significant
- posthoc = ph.posthoc_dunn(ImgPost, group_col='variable', val_col='value', p_adjust='sidak')
- if verbose:
- print(f"Performed {test_name}: test statistic = {test[0]} p-value:{test[1]}")
- return {'test':test_name, 'result':test, 'posthoc':posthoc}
Aggregate_PAZ_Data.py at commit 93478cf, under GPL-3.0 · at the source
Overview
- Department of Neurobiology, Harvard Medical School, Boston, United States
- Department of Neuroscience and Institute for Translational Neuroscience, New York University Grossman School of Medicine, New York, United States
- Department of Biology, Brandeis University, Waltham, United States
Abstract
In presynaptic nerve terminals, the endocytic apparatus rapidly restores synaptic vesicles after neurotransmitter release. Many endocytic proteins localize to the periactive zone, a loosely defined area adjacent to active zones. A prevailing model posits that recruitment of these endocytic proteins to the periactive zone is activity-dependent. We show that periactive zone targeting of endocytic proteins is largely independent of active zone machinery and synaptic activity. At mouse hippocampal synapses and Drosophila neuromuscular junctions, pharmacological or genetic silencing resulted in unchanged or increased levels of endocytic proteins including Dynamin, Amphiphysin, Nervous Wreck, Endophilin A, Dap160/
Reproduced under the paper's license (CC BY), from the paper cited above.
Repositories
Its files are read in the Code ↔ Paper reader above.
rodallab/nmj-measurement
c25ff74ccd0c20bd917189eb4f224d779859cd7f, 9 June 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
1 file
- LICENSE, License, 674 lines
rodallab/paz-analysis
93478cfa4b1449ebf54b6008f456116bb09d7340, 22 September 2022Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
9 files
- Analysis/
Aggregate_PAZ_Data.py , Python, 361 lines - Analysis/
CentroidAnalysis.py , Python, 368 lines - Analysis/
Example_NMJ-level_analys , Jupyter, 142 linesesStats.ipynb - Analysis/
Example_PAZ_Analyses.ipy , Jupyter, 536 linesnb - Analysis/
Example_PAZ_DescriptiveA , Jupyter, 548 linesnalyses.ipynb - Analysis/
PAZ_Processing.py , Python, 35 lines - Analysis/
paz-analysis_manuscript_ , Jupyter, 1,515 linesanalyses.ipynb - LICENSE, License, 674 lines
- README.md, Text, 20 lines
The paper's code and data availability statement is in the Data section.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 7 scripts, each with its path and the digest of its content;
- no match between paragraphs and code yet;
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
Datasets cited
- zenodo:20071165, at Zenodo; found in “Data availability”
Data availability
Data points generated for this study are included in the figures. Raw numerical data used to generate all figures are available at https://
The following datasets were generated:
Emperador-Melero J. 2026. Data table for Emperador-Melero, Del Signore et al; "Deployment of endocytic machinery to periactive zones of nerve terminals is independent of active zone assembly and evoked release". Zenodo.
Emperador Melero J, Del Signore S, De Leon Gonzalez K, Kaeser P, Rodal A. 2025. Deployment of endocytic machinery to periactive zones of nerve terminals is independent of active zone assembly and evoked release: Drosophila Data. Zenodo.
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, pages, dates, 5 authors, 2 keywords, 15 MeSH terms, 4 funders, 119 references, 33 RRIDs.
Cite
This paper
Emperador-Melero, J., Del Signore, S. J., De León González, K. M., Kaeser, P. S., & Rodal, A. A. (2026). Deployment of endocytic machinery to periactive zones of nerve terminals is independent of active zone assembly and evoked release. eLife, 14, RP107276. https://
BibTeX
@article{emperadormelero
author = {Emperador-Melero, Javier and Del Signore, Steven J and De León González, Kevin M and Kaeser, Pascal S and Rodal, Avital A},
title = {{Deployment of endocytic machinery to periactive zones of nerve terminals is independent of active zone assembly and evoked release}},
journal = {eLife},
year = {2026},
month = jun,
volume = {14},
pages = {RP107276},
publisher = {eLife Sciences Publications, Ltd},
issn = {2050-084X},
doi = {10.7554/
url = {https://
pmid = {42307978},
pmcid = {PMC13275065}
}
RIS
TY - JOUR
AU - Emperador-Melero, Javier
AU - Del Signore, Steven J
AU - De León González, Kevin M
AU - Kaeser, Pascal S
AU - Rodal, Avital A
TI - Deployment of endocytic machinery to periactive zones of nerve terminals is independent of active zone assembly and evoked release
T2 - eLife
J2 - eLife
PY - 2026
DA - 2026/
VL - 14
SP - RP107276
SN - 2050-084X
PB - eLife Sciences Publications, Ltd
DO - 10.7554/
UR - https://
LA - en
ER -
CSL-JSON
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"title": "Deployment of endocytic machinery to periactive zones of nerve terminals is independent of active zone assembly and evoked release",
"container-title": "eLife",
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{
"family": "Emperador-Melero",
"given": "Javier"
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{
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"given": "Steven J"
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{
"family": "De León González",
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{
"family": "Kaeser",
"given": "Pascal S"
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"given": "Avital A"
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],
"container-title-short":
"volume": "14",
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"PMID": "42307978",
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"ISSN": "2050-084X",
"publisher": "eLife Sciences Publications, Ltd",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
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2026,
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17
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]
}
}
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