eSRRF - Supplementary Data

<p><strong>eSRRF supplementary data</strong></p> <p>The eSRRF preprint is available here:&nbsp;https://doi.org/10.1101/2022.04.07.487490</p> <p>Find the code and documentation here:&nbsp;https://github.com/HenriquesLab/NanoJ-eSRRF</p> <p><strong>1a:&nbsp;Set01a_DNA-PAINT_COS7-MT.tif</strong></p> <p>DNA-PAINT of fixed COS-7 cells with indirect immunolabeling against tubulin</p> <ul> <li>Pixelsize: 160&nbsp;nm</li> <li>Exposure time: 30 ms</li> <li>50 000 frames</li> </ul> <p><strong>1b: Set01b_DNA-PAINT_COS7-MT_bin100.tif</strong></p> <p>Dataset 1a with 100 frames binning to effectivly increase emitter density.</p> <p>eSRRF analysis parameters:&nbsp;</p> <ul> <li>M=5,</li> <li>R=0.5,</li> <li>S=1</li> <li>all frames</li> </ul> <p>&nbsp;</p> <p><strong>2: Set02_HeLa_ffDronpa-MAP4.tif</strong></p> <p>Live-cell TIRF imaging dataset&nbsp;of HeLa cells expressing ffDronpa-MAP4&nbsp;</p> <ul> <li>Pixelsize: 156 nm</li> <li>Exposure time: 40 ms</li> </ul> <p>eSRRF analysis parameters:&nbsp;</p> <ul> <li>M=4</li> <li>R=2</li> <li>S=4</li> <li>100 frames</li> <li>rolling analysis gap = 50 frames</li> </ul> <p><strong>3: Set03_COS7_PrSS-mEmerald-KDEL.tif</strong></p> <p>Live-cell HiLO-TIRF of COS-7 cells expressing PrSS-mEmerald-KDEL marking the ER lumen.</p> <ul> <li>Pixelsize: 160&nbsp;nm</li> <li>Exposure time: 5&nbsp;ms</li> </ul> <p>eSRRF analysis parameters:&nbsp;</p> <ul> <li>M=5</li> <li>R=2</li> <li>S=1</li> <li>100 fr</li> <li>rolling analysis gap = 10 frames</li> </ul> <p><strong>4a:&nbsp;Set4a_MFM_HeLa_TOM20.tif</strong></p> <p>Live-cell MFM of HeLa cells expressing&nbsp;TOM20-HaloTag labeled with JF549&nbsp;</p> <ul> <li>Pixelsize: 160&nbsp;nm</li> <li>Exposure time: 20 ms</li> </ul> <p>eSRRF analysis parameters:&nbsp;</p> <ul> <li>M=4</li> <li>R=2</li> <li>S=1</li> <li>100 fr</li> <li>rolling analysis gap = 25 frames</li> <li>3D axial offset = 390 nm</li> </ul> <p><strong>4b: Set4b_MFM_beadcalibration.tif</strong></p> <p>MFM calibration data with TetraSpeck beads immobilized on a coverslip,</p> <ul> <li>Pixelsize: 160&nbsp;nm</li> <li>z-step 60 nm</li> </ul> <p><strong>5:&nbsp;Set5_LLS_Jurkat_ER.zip</strong></p> <p>Lattice light sheet (LLS) data&nbsp;of the ER in Jurkat cells. The zip-folder contains single image stacks for each z-plane:</p> <p>98 z-planes with 100 fr per plane at 10 ms exposure time&nbsp;276 nm step size in the z-axis and 104 nm pixelsize.&nbsp;</p> <p>Each z-plane stack was process with eSRRF followed by deskewing with the LLSM plugin (https://monash-merc.github.io/llsm/docs/fiji/index.html) to recover a single 3D volume reconstruction.</p> <p>eSRRF analysis parameters:&nbsp;</p> <ul> <li>M=5&nbsp;</li> <li>R=3.5&nbsp;</li> <li>S=2&nbsp;</li> <li>100 frames</li> </ul> <p><strong>6: Set6_TIRF_NeuronCulture_MT_Skylan-NS.tif</strong></p> <p>TIRF imaging data of cultured neuron expressing Skylan-NS tagged tubulin.</p> <ul> <li>Pixelsize: &nbsp;64.7 nm</li> <li>Exposure time: 100 ms</li> </ul> <p>eSRRF analysis parameters:&nbsp;</p> <ul> <li>M=4&nbsp;</li> <li>R=5</li> <li>S=2</li> <li>200 fr</li> </ul> <p><strong>7: Set7_SDC_U2OS_Skylan-S-Actin.tif</strong></p> <p>Live-cell SDC imaging data of U2OS cells transiently expressing SkylanS-&szlig;Actin&nbsp;over a time course of 12 hours by acquiring substacks of 50 frames at 10 min intervalls.</p> <ul> <li>Pixelsize:&nbsp;247.6 nm</li> <li>Exposure time: 500ms</li> </ul> <p>eSRRF analysis parameters:&nbsp;</p> <ul> <li>M=5</li> <li>R=2.5</li> <li>S=1</li> <li>50 frames</li> </ul> <p>&nbsp;</p> <p>&nbsp;</p>