Help hints appearance - lets you choose where additional information is show when you position mouse cursor over the interface control (slider, button).

Use 64/32 bit processing server  option allows to process images in separate 32 bit or 64 bit server process. This gives the program additional address space and allows to process larger images (100Mpixel and more). Moreover, on 64 bit OS the program runs even faster. This option is available if you have X64 license of the Helicon Focus.

Show intermediate results during calculation  option enables screen updating during the processing. Please note, that this takes additional 30% of total processing time!

Automatically adjust order in the stack during calculation option tells the program to detect the order of the images when no artifacts on the edges are visible. I.e. the nearest image is processed first.

Play sound for events  option lets you choose if you want to hear beep after long operations.

Ignoring the EXIF information option can be useful if you do not want to include EXIF in the output image.

The controls on this tab defines how adjacent images in the stack should be adjusted.

Vertical position  defines maximum vertical shift between two images in % of their width.

Horizontal position  defines maximum horizontal shift between two images in % of their width.

Rotation  defines maximum angle between two images in degrees. For microscope shots this is usually not needed.

Magnification  defines maximum difference in size between two images in % of their width.

Brightness  checkbox defines whether brightness of the adjacent images should be normalized.

Interpolation method lets you choose the algorithm for resampling the image during alignment process. Slower methods process more neighboring pixels and better preserve details. The difference between bicubic and more advanced methods is marginal.

Depth map feathering defines the degree of smoothing of the depth map. Method B searches for the focused areas in the source images. If these areas are combined without smoothing their edges, you may see seams on the resulting image between focused areas from different source images. So low values may result in noticable seams, higher values may give blurry areas where two focused areas are mixed together.

RAW tab:

The Raw format select contains all RAW formats supported by the program. You can set parameters for each RAW format individually. Please select the RAW format to see which parameters are available.

The Method  select contains the list of RAW converters. Helicon Focus includes three RAW converters: embedded, DCRAW and Adobe RAW/DNG converter. They use different algorithms and you should try which one provides best output for your camera. DCRAW and Adobe DNG converters can be updated manually. Please read more about here.

The Convert to DNG first (with Adobe DNG Converter)  checkbox forces the program to convert RAW file to DNG using Adobe DNG converter as the first step. This is useful if embedded converter or DCRAW do not support RAW format but provide better interpolation methods (AHD).

Parameters for RAW development without manufacturer's SDK:

The Demosaic method select lets you choose between linear, medium quality (VNG) and highest quality (AHD) methods of interpolation. AHD will sometimes result in fewer color artifacts around sharp image edges, but it can be applied only to some RAW formats.

The Adjust contrast  checkbox  tells the program to clip shadows and highlights to increase overall image contrast. Some minor details in shadows and highlights may be lost.

The Use camera white balance  checkbox lets the program use information about white balance which is available in the RAW file. Otherwise no color correction is performed.

The Use CIECAM02  checkbox controls a type of color algorithms used during digital camera raw processing.

CIECAM02 is a color appearance model that describes the transformations
between colorspaces where the overall characteristics of the scene are taken into
account.  If not checked a more precise method is used that offers less scene characteristic adjustment than CIECAM02 does, but frequently provides better image characteristics in dimly lit portions of a high dynamic range image.

The Set white balance as on the thumbnail checkbox makes the program use a thumbnail as a source of white balance and contrast information. 

Camera manufacturers often hide and encrypt white balance information. Thumbnail is generated by a camera and often it is more adequate than the converted raw file. Please note that this operation is performed on the final stage of RAW development so all previous options may be completely overridden.

Canon RAW parameters:

The Method  select contains the list of RAW converters. Helicon Focus includes three RAW converters: embedded, DCRAW and Adobe RAW/DNG converter. They use different algorithms and you should try which one provides best output for your camera. DCRAW and Adobe DNG converters can be updated manually. Please read more about here.

The Convert to DNG first (with Adobe DNG Converter)  checkbox forces the program to convert RAW file to DNG using Adobe DNG converter as the first step. This is useful if embedded converter or DCRAW do not support RAW format but provide better interpolation methods (AHD).

The Use camera defaults  checkbox defines if the Canon SDK’s default processing is used and other options  are ignored.

The Contrast select controls the image contrast.

The Color depth select controls the image color depth.

The Enhancement select controls the performed enhancement of the image.

The Light source select controls the lighting source assumption made during image
processing.

Kodak RAW parameters:

The Light source select controls the lighting source assumption made during image
processing.

The Exposure bias select defines the exposure gain to use for the image being opened. You  may try to use negative values to save overexposed highlights.

The Color reproduction select controls a color accuracy during the development process.

The Final processing select defines a saturation of the image. Portrait mode produces less saturated look when capturing images of people.

Nikon RAW parameters:

The Use Nikon SDK checkbox defines if Nikon libraries should be used to open a RAW file.

The controls on this tab defines how adjacent images in the stack should be adjusted.

Enable cache for raw images  checkbox allows the program to store temporary TIFF files to increase speed of opening  RAW files.

You can activate the navigation panel using View->Navigation panel menu command.

You can perform the following operations in the navigation panel by right clicking the image or by pressing on the menu icon ():

Select all command marks all images in the folder.

Unselect all command clears all marks, none of the images become selected.

Invert selected command changes the state of image to the opposite (selected->unselected, unselected->selected). 

Add selected to queue command adds marked images to the queue with the current settings.

Rename selected command  let you rename one or group of files using template. For example, you can rename all your files this way: "2005.06.25-The Beach (13)", so that your files are always shown sorted by date.

Copy selected command copies the marked files to the selected folder.

Move selected command moves the marked files to the selected folder.

Delete selected command moves the marked files to the trash-bin.

Lossless rotate commands rotate the image and save it with the original date and time. The operation is lossless so JPEG quality does not deteriorates. RAW files cannot be rotated by this function.

Auto rotate (lossless) command analyzes the image and tries to define its orientation. The command  assumes that the upper part of the image should be brighter than the bottom part. The program checks only images in original "landscape" orientation and ignores already rotated images.

Refresh list command updates the thumbnails and can be useful if you manually delete or rename files outside of the program.

Recent folders  command (available from the navigation panel toolbar ) remembers the list of last folders from which the image was open.

Folder tree  command (available from the navigation panel toolbar ) opens the list with the folder tree so you can see where you are located now and choose another folder.