DOI: 10.5281/zenodo.14637567
title: Raw data of spatial and temporal profile of output beams and images of fluorescent spheres and HEK293 cells obtained by STED holographic endoscope

description: The following files are in



Hierarchical Data Format version 5 (HDF5), which can be opened using, for example HDFView software, or

.dat, which can be opened using, for example Notepad


HDR_Axial_Fig_1.hdf5 - Axial extent high-dynamic-range images of pulsed excitation focus, pulsed vortex beam, and pulsed bottle beam through step-index multimode fibre (MMF), graded-index MMF, and endcap fibre, used in Figure 1 and Supplementary Figure S1.The file contains 9 datasets.Dataset name: [Fibre]_[Beam] [Fibre] = 'SI', 'GIF', or 'Endcap' | [Beam] = 'Excitation', 'Vortex', or 'Bottle'

HDR_focal_plane_Fig_1.hdf5 - Cross-section High-dynamic-range images of pulsed excitation focus and pulsed vortex beam, through step-index MMF, graded index MMF, and endcap fibre, used in Figure The file contains 6 datasets.Dataset name: [Fibre]_[Beam] [Fibre = 'SI, 'GIF, or 'Endcap' | [Beam] = 'Focus', or 'Vortex

Temporal profiles from Figure 1. Each file contains the number of photon counts per time-bin. File header contains the size of the time-bin in nanoseconds under the value '#ns/channel'.focus_pulsed_endcap.dat - pulsed excitation focus through endcap fibrefocus_pulsed_GIF.dat - pulsed excitation focus through graded-index MMFfocus_pulsed_SI.dat - pulsed excitation focus through step-index MMFvortex_pulsed_endcap.dat - pulsed depletion vortex beam through endcap fibrevortex_pulsed_GIF.dat - pulsed depletion vortex beam through graded-index MMFvoltex_pulsed_SI.dat - pulsed depletion vortex beam through step-index MMF

Images of single 400nm fluorescent sphere from Figure 2. Each file contains a single dataset with name 'Image'.m2_p0.hdf5 - image in diffraction limited regime (excitation focus)m2_p153.hdf5 - image in STED regime (excitation focus + depletion vortex beam)m2_p153_b.hdf5 - image of STED background (no excitation focus, just depletion vortex beam) [subtract to m2_p153.hdf5]

Images of 400nm fluorescent sphere cluster from Figure 2. Each file contains a single dataset with name 'Image'.cluster.hdf5 - image in diffraction limited regime (excitation focus)cluster_st_new.hdf5 - image in STED regime (excitation focus + depletion vortex beam)cluster_st_new_b.hdf5 - image of STED background (no excitation focus, just depletion vortex beam [subtract to cluster_st_new.hdf5]Fluorescence decay / Time-correlated single-photon counting histogram from a 500 nm fluorescent nanosphere measured at two STED beam powers (0mW and 107mW) from Figure 2. Each file contains the number of photon counts per time-bin. File header contains the size of the time-bin in nanoseconds under the value '#ns/channel'.p0.dat - excitation focus + STED beam power of 0mWp153.dat  - excitation focus + STED beam power of 107mWImages of HEK293 with STED holographic endoscope. Actin stained with Alexa Fluor 488 Phalloidin.Panorama image of Figure 3 composed of 4 images. Each file contains a single dataset with name 'Image'.HEK293_full_FOV5_090823_1515.hdf5HEK293_full_FOV5_1_090823_1551.hdf5HEK293_full_FOV5_2_090823_1557.hdf5HEK293_full_FOV5_3_090823_1601.hdf5The raw data from the previous images are contained in the files with same name but terminating in '_raw' (example: HEK293_full_FOV5_090823_1515_raw.hdf5). Each of these files contains 4 datasets:MarkerCode - if MarkerCode == 2 and isMarker == True, excitation focus and depletion vortex beam move to the next scanning positiondTime - photon time of arrival with respect to excitation laser sync channelisMarker - boolean, indicating if the time value corresponds to a marker or notisPhoton - boolean, indicating if the time value corresponds to a photon or notAdditional images and raw data. Datasets are organised according to the previous files.HEK293_diff5_090823_1518.hdf5 - image in diffraction limited regime (excitation focus)HEK293_diff5_090823_1518_raw.hdf5 - raw data of image in diffraction limited regime (excitation focus)HEK293_sted5_090823_1526.hdf5 - image in STED regime (excitation focus + depletion vortex beam)HEK293_sted5_090823_1526_raw.hdf5 - raw data of image in STED regime (excitation focus + depletion vortex beam)Inages of HEK293 with STED holographic endoscope. Sterol carrier protein 2 (SCP2) stained with enhanced green fluorescent protein (eGFP) from Figure 3. Datasets are organised according to the previous files.SCP2_full_FOV_100723_1508.hdf5 - image in diffraction limited regime (excitation focus) of full field-of-viewSCP2_full_FOV_100723_1508_raw.hdf5 - raw data of image in diffraction limited regime (excitation focus) of full field-of-viewSCP2_diff_100723_1513.hdf5 - image in diffraction limited regime (excitation focus)SCP2_diff_100723_1513_raw.hdf5 - raw data of image in diffraction limited regime (excitation focus)SCP2_sted_100723_1521.hdf5 - image in STED regime (excitation focus + depletion vortex)SCP2_sted_100723_1521_raw.hdf5 - raw data of image in STED regime (excitation focus + depletion vortex)HDR_Axial_Sup_Fig2.hdf5 - Axial extent high-dynamic-range images of pulsed excitation focus through a step-index MMF with different reference arm tuning, from Supplementary Figure S2. The file has 3 datasets: 'High_order_modes', 'Middle_order_modes', and 'Low_order_modes'.

HDR_vortex_corrected_hdf5 - Cross-section high-dynamic-range images of corrected vortex beams accross 1/4 of the endcap output focal plane. This file has a dataset named 'Foci'. This raw data is used to assess the extinction ratio of the produced depletion vortex beams, in Supplementary Figure S3, together with the python script Supplementary Code: 'extinction_ratio.py'.

Supplementary Movie 1test7_140323_1600.hdf5 - Image of fluorescent sphere cluster from Supplementary Figure SM1. The file contains a dataset with name 'Image'. The background (no excitation focus, just depletion vortex beam) is interleved with the image in the 3rd dimension.test7_140323_1600_raw.hdf5 - Raw data from Supplementary Video SM1. The file contains 4 datasets:MarkerCode - if MarkerCode == 2 and isMarker == True, excitation focus and depletion vortex beam move to the next scanning positiondTime - photon time of arrival with respect to excitation laser sync channelisMarker - boolean, indicating if the time value corresponds to a marker or notisPhoton - boolean, indicating if the time value corresponds to a photon or notThe video is obtained by increasing the time-gate starting position (i.e. image obtained from considering photons with dTime above a certain threshold [timegate_start], which is increased during the video).Supplementary Movie 2Datasets are organised according to the previous files.DMD_120723_1216.hdf5 - series of images (video) of HEK293 with GFP-labelled SCP2 obtained through reading PMT voltage while scanning with CW excitation and a DMD.SCP2_full_FOV2_100723_1611.hdf5 - image in diffraction limited regime (excitation focus) of full field-of-viewSCP2_full_FOV2_100723_1611_raw.hdf5 - raw data of image in diffraction limited regime (excitation focus) of full field-of-viewSCP2_diff2_100723_1617.hdf5 - image in diffraction limited regime (excitation focus)SCP2_diff2_100723_1617_raw.hdf5 - raw data of image in diffraction limited regime (excitation focus)SCP2_sted2_100723_1625.hdf5 - image in STED regime (excitation focus + depletion vortex)SCP2_sted2_100723_1625_raw.hdf5 - raw data of image in STED regime (excitation focus + depletion vortex)