... | ... | @@ -57,7 +57,12 @@ For the purpose of the notebooks, we will be using only 3 movies Image_Registrat |
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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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### 02_SIMA_ImageDisplay
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After importing the data, it might be useful to visualise the imported datasets (e.g. to sanity check if everything worked as expected). Example code for loading and displaying datasets are provided in the notebook 02_SIMA_ImageDisplay.ipynb.
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### Create ROIs
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The next step is the creation of regions-of-interest in the movies. SIMA provides automatic tools for ROI segmentation (see http://www.losonczylab.org/sima/1.3.2/tutorial.html#segmentation-and-rois). However, these approaches are very data specific and require a lot of fine-tuning for specific data sets. Therefore, the current setup relies on manual creation of ROIs with ImageJ or roibuddy GUI. For ImageJ, simply load the relevant image into ImageJ and use the ROI Manager to create an RoiSet file (e.g. RoiSet.zip). For roibuddy, start the program from the command prompt (`python -m roibuddy`) and then load the dataset created previously. When using roibuddy, the ROIs are saved directly with the dataset. For a detailed tutorial of the roibuddy GUI see http://www.losonczylab.org/sima/1.3.2/roi_buddy.html.
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## Remaining issues
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