Slidescans: p176

<p>This repository constains all the slidescans associated with slide block p176 for the project:</p> <p><strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong></p> <p>&nbsp;&nbsp;&nbsp; Vito RT Zanotelli<br> &nbsp;&nbsp;&nbsp; Matthias Leutenegger<br> &nbsp;&nbsp;&nbsp; Xiao‐Kang Lun<br> &nbsp;&nbsp;&nbsp; Fanny Georgi<br> &nbsp;&nbsp;&nbsp; Natalie de Souza<br> &nbsp;&nbsp;&nbsp; Bernd Bodenmiller</p> <p><em>Mol Syst Biol. (2020) 16: e9798</em><br> <a href="https://doi.org/10.15252/msb.20209798">https://doi.org/10.15252/msb.20209798</a></p> <p><em>Please cite this article if you re-use any of the data or code.</em></p> <p>Each acquisition follows the naming scheme:</p> <p>&quot;{operator}_{date}_{slideblock}_{slidescan_flo_number}{suffix}&quot;</p> <p>e.g. <a href="https://zenodo.org/api/files/024cdd60-5ab8-4c5b-9c5c-9778400d2e64/v.zanotelli_20190509_p161_025.czi?versionId=980e5ce9-6bb0-40d4-872f-992dc14081b5">v.zanotelli_20190509_p161_025.czi </a></p> <p>With:</p> <ul> <li>&nbsp;operator: the slidescan operator</li> <li>&nbsp;date: the acquisition date</li> <li>&nbsp;slideblock: the block cut to produce these slides</li> <li>&nbsp;slidescan_fluo_nr: arbitrary index. Is matched to actual slide number using the metadata file: &#39;20190506_bigstain_selection_final_if_imcalign_v1.csv&#39;</li> <li>&nbsp;suffix: <ul> <li>&nbsp;&nbsp; &#39;.czi&#39;: main slidescan</li> <li>&nbsp;&nbsp; &#39;_pt1.czi&#39;: scan of handwritten slide label</li> <li>&nbsp;&nbsp; &#39;_pt2.csi&#39;: coarse slide overview scan</li> </ul> </li> </ul> <p>Each &#39;main slidescan&#39; is usually composed of multiple &#39;scenes&#39; (regions that were scanned with high resolution). The convention is that each scene corresponds to unique cut that is independently stained. Note that scene numbering is not sequential but rather random.</p> <p>The slidescans were acquired using an AxioScan.Z1 microscope with:</p> <ul> <li>Objective: Plan-Apochromat 20x/0.8 M27</li> <li>Resolution: nominal 0.325 um/pixel</li> <li>Channels: <ul> <li>1) DAPI: Excitation Wavelength:&nbsp; 353 nm, Emission Wavelength: 465 nm</li> </ul> </li> </ul> <p>&nbsp;</p>