DOI: 10.5281/zenodo.5244550
title: Accompanying dataset for: "IBEX: An iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues"

description: These datasets were acquired using either the manual or automated IBEX multiplex imaging protocols and accompany the manuscript “IBEX: An iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues”, A. Radtke <em>et al.</em>, 2021, Nature Protocols. All image data are stored using the Imaris file format. To view these multi-channel images, you can either use one of these <strong>free</strong> viewers, Imaris viewer, Fiji. Each experiment has an associated imaging meta-data file in xlsx format and the resulting image in Imaris format. <strong>Human Jejunum (Automated)</strong> Dataset is a 24 parameter IBEX experiment performed on a human jejunum section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Thunder 3D Cell Culture microscope with a high precision (Quantum) stage, a high quantum efficiency sCMOS camera (DFC9000 GTC), and a 40x (1.3) NA oil objective. The light source was an LED8 with 8 individual LED lines for excitation with millisecond triggering. All images were captured at a 16-bit depth with the following pixel dimensions: x (0.160 μm), y (0.160 μm), and z (1 μm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.7.1.21655). <strong>Human Kidney (Automated)</strong> Dataset is a 16 parameter IBEX experiment performed on a human kidney Formalin-Fixed Paraffin-Embedded (FFPE) section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Thunder 3D Cell Culture microscope with a high precision (Quantum) stage, a high quantum efficiency sCMOS camera (DFC9000 GTC), and a 40x (1.3) NA oil objective. The light source was an LED8 with 8 individual LED lines for excitation with millisecond triggering. All images were captured at a 16-bit depth with the following pixel dimensions: x (0.160 μm), y (0.160 μm), and z (1 μm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.7.1.21655). <strong>Human Lymph Node (Automated)</strong> Dataset is a 25 parameter IBEX experiment performed on a human lymph node section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Thunder 3D Cell Culture microscope with a high precision (Quantum) stage, a high quantum efficiency sCMOS camera (DFC9000 GTC), and a 40x (1.3) NA oil objective. The light source was an LED8 with 8 individual LED lines for excitation with millisecond triggering. All images were captured at a 16-bit depth with the following pixel dimensions: x (0.160 μm), y (0.160 μm), and z (1 μm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.7.1.21655). <strong>Human Skin (Automated)</strong> Dataset is an 18 parameter IBEX experiment performed on a human skin section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Thunder 3D Cell Culture microscope with a high precision (Quantum) stage, a high quantum efficiency sCMOS camera (DFC9000 GTC), and a 40x (1.3) NA oil objective. The light source was an LED8 with 8 individual LED lines for excitation with millisecond triggering. All images were captured at a 16-bit depth with the following pixel dimensions: x (0.160 μm), y (0.160 μm), and z (1 μm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.7.1.21655). <strong>Human Liver (Manual)</strong> Dataset is a 22 parameter IBEX experiment performed on a human liver section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976). <strong>Human Lymph Node (Manual)</strong> Dataset is a 38 parameter IBEX experiment performed on a human lymph node section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976). <strong>Human Spleen (Manual)</strong> Dataset is a 25 parameter IBEX experiment performed on a human spleen section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).