With some cameras the dark signal affecting some pixels is so high that the removal of the thermal signal is not so satisfactory.

ISIS can identify these pixels, which is called "hot spots" or "hot pixels" and use specifically when processing your spectra.

You must first identify these hot pixels. Open the tab "Master images" tab. Localise "Compute a cosmetic file" tool. Give a name dark map already calculated, if possible with a long exposure time. Choose a threshold detection intensity for hot spots. The lower value, the greater number of hot pixel is find. A typical threshold value is between 100 and 500. Good value is one that allows you to find 50 to 200 hot spots in a CCD image. Give the file a name that will contain the list of hot spots coordinates. In our example, it is called "cosme"(the
full file name will be "come.lst").

To account for the presence of hot spots during the processing, just specify the cosmetic file name in "General processing" tab.

Top left, the spectrum image of 2011cj supernova of magnitude 16.0 (C11 + LISA + Atik314L camera). Exposure time is 12 x 300 seconds. The bright spots are the impacts of cosmic rays.

Below, the same image by activating a ISIS specific filter for effectively remove cosmic rays without removing actual details of the spectrum. To activate this filter, just check the option "Cosmic rays filter" in "General processing" tab.

Attention, calculation time is significantly lengthened when this option is chosen. Do not filter the cosmic rays in case of need (when observing faint objects).

In the research work to increase the signal to noise ratio you can seek to optimize the width of the binning area for extract spectrum profile.

A width of 15 to 18 pixels with LISA spectrograph mounted on a intermediate size telescope is reasonable.

For difficult situations, example of  V=16.0  SN2011cj supernova, we can try to optimize width of the binning. The impact of sky background noise is minimized.

The operation can degrade the photometric quality, but so almost imperceptible and insignificant if the spectrum is at the limit of detection. Here the width of the binning only 8 pixels (+ /-4 pixels relative to the central spectrum axis). Note that we deselected the option "Default values" beforehand.

In this example, we also modify areas of computing sky background in order to avoid including in the calculating the faint light of the home galaxy (note the asymmetry between the top and bottom of the trace of the spectrum).

Tip: After processing, you can consider the composite 2D spectrum, corrected for
distortions, and with the sky background removed. To do this, load from "Image display" tab the processed 2D image. If necessary, repeat the processing by adjust the settings if you check here
abnormality (bad angle of slant, bad computing sky background area, ...).