This folder is supposed to contain a well documented data-processing pipeline from raw Ca-images (from neuronal data) to a thorough receptive field analysis.
currently, CaImAn requires (I think) tiff files to perform memory efficient creation of memmap-files. I suppose most data comes in tiff/format, though saving in zarr/hdf5 might be way more efficient (for both, reading and writing). CHECK: are hdf5 files already implemented? what is the proper syntax then? if not: possible to implement?
The analysis pipeline consists of:
| | I. preprocessing | - I.1. median filter | - I.2. alignment / motion correction | - I.3. casting to proper type (memmap) | | II. image analysis | - II.1. [CaImAn] neuron detection & trace extraction | - II.2. [CaImAn] component evaluation | - II.3. saving relevant data | | III. analysis | - III.1. ROI matching | - III.2. place field detection | - III.3. everything else