Images with no DAPI staining as filter parameter

[Marcel-Salier]

Hi Fursham, I opened the Tiff file in the analyzor and I found that we have to put the option of which channel to use at the beginning instead of DAPI (although this will be the default). I got this that I think I can modify but not sure where to open it for that.

ValueError Traceback (most recent call last) Input In [6], in <cell line: 1>() ----> 1 obj.findSingleCells(byExperiment = True, nbins = 45, spread = 0.4, channel = None)

File ~/Documents/GitHub/ng_tools/ngtools/analyzer.py:691, in Analyzor.findSingleCells(self, byExperiment, nbins, spread, channel) 689 if channel == None: 690 channel = "dapi" --> 691 ss_array = find_SingleCells(self.data['raw'], byExperiment, nbins, spread, channel) 692 self.data['raw']['isSingleCell'] = ss_array 693 self.data['norm']['isSingleCell'] = ss_array

File ~/Documents/GitHub/ng_tools/ngtools/analyzer.py:86, in find_SingleCells(df, byExperiment, nbins, spread, channel, hue) 83 col = f"totalintensity{channel}" 85 if not col in list(df.columns): ---> 86 raise ValueError("Ops! Channel not found.") 88 if byExperiment: 89 for n, exp in tqdm(enumerate(set(df[hue])), total=len(set(df_[hue]))):

ValueError: Ops! Channel not found.

[fursham-h]

The option to set the marker channel is already in the function, and is reflected in the Notebook. Just set channel to "BrdU".

obj.findSingleCells(byExperiment = True, nbins = 100, spread = 0.4, channel = "BrdU")