@@ -227,7 +227,7 @@ This tab contains options for selecting ROIs and discarding pixels vie arbitrary
For some applications (e.g. RICS or N&B) it might be useful to subtract the background from the corrected image prior to further analysis. Pushing this button displays the average count rate (in photons per pixel dwell time) in the currently selected ROI. Alternatively, if you know the background count rate from a control experiment, you can also write the value directly in the edit box. The left edit box is channel 1, the right one is channel 2. The values displayed in the edit boxes are subtracted from the images after any correction (see Correction tab) has been carried out.
*Import ROI from .mat file* pushbutton:
ALlows importing a mask from a pre-defined .mat file.
Allows importing a mask from a pre-defined .mat file.
Correction
~~~~~~~~~~~~
@@ -463,7 +463,7 @@ For determining absolute brightnesses (kHz) with e.g. :ref:`RICS <RICS>` and :re
.. figure:: _images/MIA/VarInt.png
:figwidth: 100 %
:width: 100 %
:width: 30 %
:align: center
Variance vs. Intensity plot
@@ -480,7 +480,25 @@ For determining absolute brightnesses (kHz) with e.g. :ref:`RICS <RICS>` and :re
Spectral RICS
-------------------------------
From the menu **Open... Spectral** a user interface can be called that allows generating spectral filters and applying these to RICS data.
From the menu **Open... Spectral** a user interface can be called that allows generating spectral filters and applying these to RICS data. Alternatively, the Spectral UI can be opened from the command window by typing “Spectral”.
For spectral filtering of data, single-species reference data can be loaded via **Load -> species data** (highlight #1). When selected (highlight #2), the relative frequency of photons detected in the different channels can be observed in the graph. By pressing the **Create filters** pushbutton when both reference species are still selected (highlight #3), filter patterns are created.
Data can be loaded one by one via **Load -> data directly** (highlight #1). In order to process the image series with the spectral filter, go to the **Filters** tab (highlight #4).
.. figure:: _images/MIA/Spectral.png
:figwidth: 100 %
:width: 100 %
:align: center
The Spectral User Interface
Select the filters on the **Filters** tab by pressing the “+” key (highlight #4) and pressing the **Save filtered data** pushbutton (highlight #5). This action creates two .tif files, one weighted towards the green and one towards the red species. Specifically, the signal intensity of each spectral bin of each pixel is multiplied with its corresponding weight, and every weighted pixel is summed up over all spectral bins [Schrimpf2018]_.
Batch processing is possible via load -> data to database.
The newly generated weighted .tif files can be opened and further analysed from Mia by choosing the **Load... weighted TIFFs** option from the menu.
