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### Example data
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The notebooks have been developed with calcium imaging movies acquired with ScanImage by the Svoboda lab. The data are part of a dataset that is publicly available here: http://crcns.org/data-sets/ssc/ssc-1
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For the purpose of the notebooks, we will be using only 3 movies Image_Registration_4_an197522_2013_03_08_main_001.tif - Image_Registration_4_an197522_2013_03_08_main_003.tif. Each movie contains data from two channels (GCamP, td-Tomato) interleaved.
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### 01_SIMA_DataImport
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The first notebook imports raw imaging files into a SIMA dataset. The dataset is saved and, optionally, motion correction is performed. Details are described in the relevant comment sections of the notebook. To adjust this notebook for other imaging data, it should be sufficient to change the parameters in the second code cell (Specify file paths and names). This step will create a new dataset folder, relative to the input data, called analysis.sima (the name can be changed, but it should always end with .sima). Note that the dataset folder only **links** to the original image files. **Therefore, the image files must always reside in the same location relative to the analysis folder!** If motion correction is also performed, a second output folder analysis_hmm.sima will also be created.
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###
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## Remaining issues
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