Influence of Yokukansan on refractive index of neuroblastoma cells - dataset

<p>This dataset contains 3 sets with files connected to holographic tomography (HT), fluorescence microscopy (FM) and Raman micro-spectroscopy (RmS) measurements. All measurements are from experiment on SH-SY5Y neuroblastoma cells with treatement of diferent doses of Yokukansan (YKS - Chinses herbal medicine herb). Measurements were carried out in Nencki Institute of Experimental Biology and University of Warsaw.&nbsp;</p> <p><strong>For HT:</strong><br> All files are *.mat files</p> <p>HT_3D_RI - in the file there are values of RI of cells (named in order: &quot;RI3D_DoseTime&quot; for ex. &quot;RI3D_1mg25h&quot;)&nbsp;<br> HT_LD_volumes - in the file, there are values of LD volumes and whole cell volumes for cells (named in order: &quot;LD_DoseTime&quot; for ex. &quot;LD_1mg25h&quot;)</p> <p><strong>For FM:</strong><br> File is an *.xlsx</p> <p>In the file there is a spreadsheet with data of mean intensity of Hoechst staining signal in cells measured with FM.&nbsp;<br> There are results from 3 repetition of the experiment (Day 1, 2, 3). In one experiment there were measurements of 8 doses (0,5, 1, 2, 4, 5, 6, 7, 8, mg/ml) in 4 time points (after 24h, 48h, 72h, 6 days). There is also control measurement values for each day.</p> <p><br> <strong>For RmS:</strong><br> There are three *.npy files and one *.txt</p> <p>*.npy files containing the raw hyperspectral cube of the SH-SY5Y neuroblastoma cells in the form of the numpy three-dimensional array (named in order: &quot;RmS_DoseTime&quot; for ex. &quot;RmS_4mg24h&quot;).&nbsp;Two first dimensions correspond to the spatial position of the recorded spectra and the last one contains intensities for the Raman shift range.&nbsp;The measurement was performed with spatial resolution of 0.5 &micro;m.&nbsp;Information about the Raman shift values for which the spectra were recorded can be found in the Raman_shift_values.txt file.&nbsp;</p> <p>Code example:<br> import numpy as np<br> hypespectral_cube = np.load(&#39;control.npy&#39;) &nbsp; # Loading the data<br> R_shifts = np.loadtxt(&#39;Raman_shift_values.txt&#39;) # vector of Raman shifts<br> single_spectrum = hypespectral_cube[x,y,:] # gives Raman intensity recorded at x*0.5 &micro;m, y*0.5 &micro;m position.&nbsp;<br> intensity_map = hypespectral_cube[:,:,Rshift_index] # gives the intensity image for the specific Raman shift value defined by R_shifts[Rshift_index]</p>