How do I Fix thin black likes in the image

@dsalman1 Hi Dean, let me start with writing this: our product is called AstroPixelProcessor, not Astro Pixels. We generally abbreviate it to APP, not AP.

Having said that, from the looks of the screenshot, it seems that you are not using any flats. Does it help if you use those? Apart from that, what version of APP are you using? Is the data stored on the internal HD of your computer or on an external one? If external, does it help if you put them on the internal HD? APP is quite I/O heavy and doesn't handle data stored on an external HD well, unless it is an SDD.

Adding to that; are you using calibration files like darks and bias? Could be a pattern that shows up there.

Thanks guys. This was just a raw image to show the lines.   I use BIAS darks and flats and this pattern is in all the files.  I do not use dark flats because the flats are very short however I wonder if I need to do that because the lines are in the flats, just realized that now.   These lines so vary slightly so that could be why just standard calibration may not be working.  I am new to APP and have used a number of programs since i switched from film to CCD 20 years ago.  One reason I wanted to try APP is the interface is much nicer and it seems to work very with with one shot color cameras.   I need to work with the rejecting and advance features with APP more which I am doing during this 30 trial.  I recommended this program to my friend with the same camera FLI 9000 and his 24 inch.  The response the forum is great and I am capturing more image data from the telescopes where I work, but I am close into deciding to purchase APP.     

Thanks Dean,

So are you sure all calibration files are indeed applied to the lights? You can see this in the list where all lights should get a "MD, MB, MF" for MasterDark, MasterBias and MasterFlat, added to their filename. You can also check if calibration will work ok, by loading in the lights and calibration files and then selecting "l-calibrated" on top of the image viewer. This will correct the currently selected light and show it corrected, you can then check if that works ok before going through the lengthy process of APP.

Thanks Vincent, still pretty new to APP so i will review more closely