Raw data of spatial and temporal profile of output beams and images of fluorescent spheres and HEK293 cells obtained by STED holographic endoscope

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)