An ImageJ/FIJI Preprocessing Workflow for Multi-Series Confocal Microscopy Datasets Prior To CellProfiler Analysis
By onA workflow using ImageJ/FIJI aims to create three-slice MIPs from multi-series .czi files to capture weak signals. It involves extracting datasets, creating projections, and saving images for efficient analysis in CellProfiler.
Primary Tabular Data for article “CHCHD2 mutant mice link mitochondrial deficits to PD pathophysiology” by Liao et al
By onMitochondrial dysfunction is linked to CHCHD2 mutation, causing altered protein interactions, glycolysis, and ROS, plus α-synuclein aggregation, and neurodegeneration. CHCHD2 accumulation leads to mitochondrial impairment and PD progression.
Holographic calibration
By onThis is the standard protocol for 2-photon holographic calibration with In vivo Ultima Bruker microscope through GRIN lens used for Rodrigues-Vaz and Athalye et al, 2025.
Imaging using 2-photon microscope through GRIN lens
By onThis is the standard protocol for 2-photon imaging with Bruker microscope through GRIN lens used for Rodrigues-Vaz and Athalye et al, 2025.
Histology Albarran et al 2025
By onHistology protocol for Albarran et al 2025 that was adapted from Fushiki et al 2024 , to quantify Th+ cells.
Albarran et al Histology dataset
By onDataset from a whole-brain imaging experiment showing recombinase expression in different brain regions using knock-in lines (D1-Cre, A2a-Cre, D1-FlpO, A2a-FlpO, DAT-FlpO) crossed with fluorescent reporter lines.
Cryo-electron tomography of thinned synapses
By onProtocol for cryo-ET of thinned synapses in rat neuron cultures is detailed. Cryo-FIB milling creates thin samples for high-resolution imaging. Synapse targeting with and without cryo-FLM correlation is explained.
Single particle analysis of α-Synuclein fibrils
By onAggregates of α-Synuclein are linked to Parkinson’s, multiple system atrophy, and Lewy body dementia. This protocol outlines near-atomic resolution structures of these amyloid fibrils using cryo-EM single particle analysis.
Preparing primary sandwich hippocampal neuron cultures for cryo-electron tomography
By onSandwich hippocampal neuron cultures have low cell density and few glial cells, making them ideal for targeting neurons for cryo-electron tomography.
Single particle analysis datasets of in vitro grown aSyn filaments
By onDataset includes cryo-EM micrographs of a-Synuclein fibrils with WT and mutant forms (G14R, K58N) found in patients.
Tomogram of aggregate in AgDD-sfGFP-expressing HEK293 cell 10 min post aggregation induction
By onAgDD protein aggregation can be controlled for cellular studies. A cryo-electron tomogram shows an AgDD aggregate in a HEK293 cell 10 min post-aggregation induction.
Tomogram of aggregate in AgDD-sfGFP-expressing HEK293 cell 6 h post aggregation induction
By onAgDD protein aggregation in HEK293 cells can be temporally controlled for studying cellular effects. A cryo-electron tomogram shows AgDD aggregate formation 6h post-induction.
Cryo-EM map of in vitro grown G14R alpha-synuclein fibrils
By on3.0 A resolution cryo-EM map obtained from recombinant a-synuclein fibrils carrying the G14R mutation recently discovered in a patient of a complex neurological disease.
Cryo-EM map of in vitro grown WT alpha-synuclein fibrils
By onCryo-EM density map of recombinant WT a-synuclein fibrils at 2.7 A resolution.
Cryo-EM map of recombinant K58N alpha-synuclein fibrils
By onCryo-EM map obtained from recombinant a-synuclein fibrils carrying the K58N mutation recently discovered in a patient of Parkinson's disease.
3d Structure of the Human Hippocampus by holo-tomography: Alzheimer Disease vs Control
By onDataset from ESRF's ID16A beamline includes high-res X-ray nano-tomography data of human brain samples with Alzheimer’s, Parkinson’s, and control cases, along with acquisition details for reuse.
Replication Data for: 3D imaging of neuronal inclusions and protein aggregates in human neurodegeneration by multiscale X-ray phase-contrast tomography
By onDataset from DESY, GINX Beamline, Germany offers X-ray phase-contrast tomography volumes of human brain tissue for 3D analysis and reproducible imaging workflow correlation with histological sections.
Sample Preparation Correlative XPCT – Histology
By onThis protocol describes the placement of samples for XPCT and preparation of correlative histological analysis after the measurement.
Protocols Suite — SH-SY5Y / iCell® Neurons / High-Content Imaging
By onMaintenance of SH-SY5Y cells with SNCA overexpression in DMEM/F-12, differentiation with RA/BDNF, and culture of iCell DopaNeurons with SNCA mutation. Treatment and immunostaining for downstream assays using specific protocols and analysis tools.
Mouse brain immunohistochemistry – colorimetric analysis
By onProtocol for colorimetric analysis of mouse brain immunohistochemistry is described.
