HeliconFocus is a program that creates one completely focused image from several partially focused images by combining the focused areas. The program is designed for macrophotography and optical microscope image processing to cope with the shallow depth-of-field problem. Helicon Focus also aligns images as objects often change their size and position from shot to shot. This function is especially important for macrophotography.

	First plane	Last plane	Combined image
Optical microscope, 100x magnification, 15 images
Digital camera, DOF: 2cm-3m, 24 images

more samples>>

Helicon Focus Lite (basic version):

- automatically adjusts and resizes images (important for stereomicroscopes and macrophotography);
- processes an unlimited number of images in the stack;
- has no limitation on image resolutions (you need at least 512M RAM to work with 8Mp+ images);
- supports "dust map" to automatically remove black points from the resulting images;
- automatically adjusts brightness of the adjacent images;
- reads RAW, 8bit and 16bit TIFFs, JPEG, JPEG 2000, BMP, etc;
- writes 8bit and 16bit TIFFs, JPEG, JPEG 2000, BMP;
- adds text and scale bar (v.4.0+);

samples>>   download>>   purchase>>  forum>> 

Helicon Focus Pro (advanced version):

samples>>   download>>   purchase>>  forum>>

Download

Open program home page http://www.heliconfocus.com and follow the link to the download page

System requirements

The recommended system configuration to process a 4-5-megapixel images is:

• Windows 9x, ME, NT, 2000, XP
• Pentium-III class machine or higher
• 256 MB RAM or higher
• True color display, resolution 1024x768 or more

Minimum system requirements are:

• Windows 95
• Pentium-I class machine
• 64 MB RAM
• Hi-color display, resolution 800x600

Installation

Start installation program and follow instructions.

Command line mode

Helicon Focus can be called from other programs with parameters in command line

Here is the list and formats of command line parameters:

Registration

During a 30 day evaluation period all features of Helicon Focus are activated in all versions (Lite, Pro).
 

• To use advanced features after evaluation period without promotion text, one should purchase a license from our web site  (http://www.heliconfocus.com).
• After that you will receive a registration key, which should be pasted into Helicon Focus menu->Help->Registration dialog. The program will check the key and will unlock your copy.
  

Files

What can I do here?
You can browse folders by selecting them in the file tree on the right.
You can select images that you want to process by setting  the red mark against each image.

What do I do next?
Switch to Parameters tab to fine tune processing options.
Or press Run button to process selected images with the current parameters.

General workflow

Step 1. Creating stack of images

You are supposed to work with an optic microscope and a digital camera, or with additional macrolens on digital camera.

Method 1. (Microscopes or  camera on rails):

• Set your digital camera to manual focusing mode(!!) and set the focus to infinity.
• Manual mode (shutter speed and exposition) is also preferable to avoid fluctuation of brightness.
• Adjust the microscope to make the topmost area of the object sharp.
• Take a shot. Use the remote control (if available) to minimize  shaking of the camera.
• Using the fine adjustment controls, the shift sharp area a little down.
• Take a shot.
• Use small, roughly regular steps while adjusting the mircoscope and taking shots. It is better when sharp areas overlap.
• Take shots until you reach the lowest area of the scene.
   

Method 2. (Camera on tripod):

• Set your digital camera to manual focusing mode(!!) .
• Manual mode (shutter speed and exposition) is also preferable to avoid fluctuation of brightness.
• Focus on the nearest  part of the object.
• Take a shot. Use the remote control (if available) to minimize shaking of the camera.
• Manually move focus of the camera a bit to shoot next part of the object.
• Take a shot.
• Use small, roughly regular steps while moving the focus and taking shots. It is better when sharp areas overlap.
• Take shots until you reach the utmost area of the scene.
   

Step 2. Loading images to Helicon Focus

• Copy images from the camera to your computer
• Start Helicon Focus via menu, quick launch or desktop icon.
• Open the folder with the images in the file tree on the right. Or add files with File->Add new item(s) command. Note that multiple selection is possible the the Open File dialog. Click the first file and Shift-click the last file to select all of them.

If the file contains EXIF information, then it will be shown just below the image preview.

Helicon Focus supports JPEG, TIFF, BMP, PSD and various RAW formats with 8 and 16 bits per channel.

Step 3. Combining images

• Start calculation by pressing Run button.
• Review the resulting image, run again with new parameters if needed.

Read Parameters page to know more how to fine tune combining parameters.

Step 4. Saving the output file

• Switch to Saving tab to save the output image to disk, email or print it.
• Click on the image in the output list you want to save, then use the menu command File\Save, toolbar icon or hotkey Ctrl-S.
• In the save dialog select the file format (JPEG, BMP, TIFF, JPEG2000, PSD) and set the name of the output file.

JPEG quality control uses the Photoshop scale (7-12) and Photoshop "Save for the Web" scale (52-100%)

If the input files have 16 bit per channel, then output TIFF will also be written with 16 bit quality.

Preferences window

To open the Preference window use the menu command "View->Preferences" menu command.

Accelerator for dragging the image - makes navigation in the main window more efficient by moving the image faster than the mouse. Help hints appearance - lets you choose where additional information is show when you position mouse cursor over the interface control (slider, button). 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.

Autoadjustment tab of the Preferences 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.

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. 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. To get more information about VNG and AHD methods, please read http://www.aim-dtp.net/aim/digicam/dcraw/vng-ahd-comparison.htm 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 Use camera defaults  checkbox defines if the Canon SDK’s default processing will be used and other options  will be 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.

Cache tab of the Preferences 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. Enable cache for thumbnails  checkbox allows the program to thumbnails for quicker browsing of the images.

Navigation Panel

The Navigation panel shows the thumbnails of the images in the current folder. 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. Parent folder  command (available from the navigation panel toolbar ) let you jump to the parent folder. All marks in the current folder will be lost. Small/Normal thumbnail  command (available from the navigation panel toolbar ) changes vertical size of thumbnails in the navigation window.

Parameters

What can I do here?
You can fine tune Radius and  Smoothing parameters to get the best output image. More>>
You can exclude some images from processing by removing  the red mark against the image in the upper list.
Click on output  listing to view all available output images in the lower list to choose the best one. 

What do I do next?
Press Run button to merge selected images with the current parameters and get resulting image.
Press Add to queue button to process selected images later in batch mode.  More >>
Switch to Retouching tab to manually fix defects of automatic processing.
Switch to Saving tab  to save the output image to disk, email or print it.

Options:

Radius is the most important parameter for processing. It defines the size of area around each point which is used to define if the point is focused or not.

If your image has fine details, most probably low level of radius (3-6)  would give the best results.

If the image consists mostly of the coarse lines, then you should try higher values (10-15).

The Smoothing slider defines how the focused parts are combined. Low level produces sharper image, but transition areas may have some artifacts. High level of smoothing will result in a bit blurry image without visible transition areas.

Add dust map command let's you select and import file with the dust map. Use as a dust map command lets the program interpret the selected image as a dust map.

Retouching

What can I do here?
You can copy focused areas from the manually selected source images to the resulting image.
You can clone any areas on resulting image from one place to another.

What do I do next?
Switch to Saving tab  to save the output image to disk, email or print it.

How to use retouching brushes to remove artifacts?

Sometimes the program creates artifacts on the final image. Usually it is halo around bright edges on the smooth background.

Source image with well focused object	Final image with artifacts	Partially fixed final images

To fix such kind of problem use Copy source brush . Select the source image where the object is focused and copy pixels to the resulting image to delete artifacts.
Undo: keep Shift pressed to paint with Erase changes brush.

In many cases the program does not have enough information to construct the perfect image: object on the foreground masks objects behind it (see leftmost image below).

The object on the background  is focused	The object on the foreground  is focused	Resulting image with small artifact  (pointed by green arrow)	Cloning applied to fix the problem

In this case the only solution is to apply Clone brush to reconstruct missing details. Undo: keep Shift pressed to paint with Erase changes brush.

Shortcuts:

Use Right mouse button to switch to the source image and to drag the image.

+ Use Left mouse button and Shift key to erase changes.

Use Mouse wheel to change brush size.

Common parameters:

Brush size slider defines the size of the brush in pixels.

Brush hardness  slider defines the form of the brush edge.

Edge sensitivity slider makes the brush smarter: the mouse pointer is changed to double circle (), the effect is applied to external circle only if the color is similar to those in the internal circle. On the following image  the left point was made with this option, the right one without edge detection.

Brushes:

  +   Use   Ctrl+Left click  to set the new source area. This can also be done by pressing Clone new area button.

Copy source brush

This brush lets you copy the same area from one of the source images to the resulting image.

If you see artifact on the resulting image, you can choose the source image where this area is well focused and copy the area to the output. 

Erase changes brush

This brush is designed to selectively erase the effect of the previous brushes.  You can restore the pixels to the state they were before retouching.

If you are painting with other brushes and want to remove only some strokes, keep Shift pressed to paint with Erase changes brush.

To show or  hide Help panel of Helicon Focus use button from the toolbar or View->Help panel command in the main menu.

Text/Scale

What can I do here?
You can add scale bar and several text lines to the resulting image.

What do I do next?
Switch to Saving tab  to save the output image to disk, email or print it.

Controls to add scale bar

The Add scale check box shows if the selected scale bar is visible or not. The Invert color check box lets you choose in which color the scale bar should be drawn (black or white). The Select scale button opens the dialog with the list of all scale bars available. If you need some other type of the scale bar you can send us your request or you can add it yourself. If you want to create your own scale bar, please follow these rules: 1. Use PNG format to store the image with scale bar. 2. The size of the image should be about 1000-2000 pixels wide. 3. Do not use smoothing (antialiasing). The edges of the lines and text should be sharp. Otherwise the scale bar will have thin outline. 4. Place your file to "\images\Helicon Focus Scales"  subfolder.

To show or  hide Help panel of Helicon Focus use button from the toolbar or View->Help panel command in the main menu.

Saving

What can I do here?
You can  save the output image to disk, email or print it.
You can create web animation for presentation purposes.
 

What do I do next??
Switch back to Files tab so select other images to process.
Or switch to Parameters tab to fine tune processing options.

  Save to disk action

The File name edit box contains the name of the file to be saved on the disk. By default the result name is formed by source image name and suffix (HF) to not accidentally overwrite the original image.

The File type select box lets you choose among JPEG, TIFF and other file types.

The Quality  select defines the quality level for JPEG and JPEG2000 file types ("lossy" formats).  Please note, that TIFF, BMP provide lossless storage of the information. If you plan further processing of the image, it is recommended to store it in lossless format (TIFF) or at least in 100% JPEG. If you plan to print the image, 10 (80%) quality is usually sufficient.

The Calculate size  button shows the size of the file for the selected file type and quality level. If the file is too large, try to lower JPEG quality. If this does not help, switch to Resize filter and downsize the image to lower resolution. If you plan to email this image, it is recommended to keep the file size at 50-200KB and downsize it to 800-1280 pixels on greater side.

Send by email action

Choose this action to send the result image by email. The program will try to use your default mail client to send this email.

The Change image size select box lets you change the resolution of the image to reduce its size. To check new file size use "Calculate file size" button.

To show or  hide Help panel of Helicon Focus use button from the toolbar or View->Help panel command in the main menu.

Dust map

"Dust map" is a special function to remove black points from the images caused by dust on the sensor or dust in the optical system of the microscope.  The dust points often leave a dark "tracks" on the resulting image. Please have a look at the 100% crop of the sample image (provided by Phil McCollum):

"Dust map" function is OFF	"Dust map" function is ON

To use this function follow these steps:

1. Prepare "white frame".  After (or before) you shot all other images, make unfocused (!) shot of the white surface, so that dust on the sensor can be easily identified.
2. Start Helicon Focus, add stack of images.
3. Add  dust map using "File->Add dust map" menu command.
4. Run combining process.

Please note, that dust map should have the same dimensions as all the other images in the stack.

Here is an example of the "white frame" or dust map (provided by Phil McCollum):

And here is the dust map processed by Helicon Focus to reveal small dust points:

Micro panorama

What can I do here?
You can stitch several images into micro panorama.

What do I do next?
Press Run button to stitch images with the current parameters and get resulting image.

Workflow:

• Set your digital camera to manual exposure mode (shutter speed, aperture, ISO). Otherwise images may have different brightness.
• Position the object of your interest to shoot the upper left part of it.
• Take a shot. Use the remote control (if available) to minimize camera shaking.
• Move the object to the left so that adjacent shots overlap by 20-30%.
• Take a shot.
• Move the specimen horizontally, then down to start the next row.
• Take shots until you cover all the object.

Tips:

Please note that panorama is available only in Pro and Multiprocessor versions. 

Micro panorama function is designed to stitch images made through the microscope. It may fail to stitch images that are made by camera rotation on the tripod.

You can shoot each row always from the left to the right or you can shoot odd rows (1,3,5,...) from the left to the right and even rows (2,4,6,...) in reverse direction.

The program aligns images based on the parameters set in  Autoadjustment settings. The program only shifts images to align them, no magnification or rotation is applied.

Options:

The Rows  control lets you choose how many rows your panorama will have.

The Columns  control lets you choose how many columns your panorama will have.

The Overlapping for rows slider defines how adjacent rows overlap.

The Overlapping for columns slider defines how adjacent columns overlap.

The Crop margins checkbox defines if the resulting panorama should be cropped to leave only filled with pixels rectangle.

The Reset position of images button lets you restore position of the images after you dragged them with the mouse.

The Sequence: normal button should be selected you if you shot every row of images from the left to the right.

The Sequence: zigzag button should be selected if you shot odd rows from the left to the right, even rows - from the right to the left.

The Smooth seams slider defines the width of seams with gradient transparency.

The  Pro version of Helicon Focus offers you a powerful feature of processing many image stacks in batch mode.

On the Parameters tab you can either process the images at once ( ) or you can queue the task and process several task later ( ).

Editing queue and starting batch processing

You can check which tasks were added to the queue. Press F7 or call the menu command File\Queue... to see the list of tasks to be processed.

In the Queue dialog you can remove one or all tasks and start batch processing with Start button.

Setting queue options

Before starting the batch processing please check the parameters on the Options tab in the Queue dialog.

Here you can select the output file format, the output directory and the output name.

By default the output images are saved in the subdirectory of source directory with the name "Focused".

The output name is created based on date, time and processing parameters.

Starting the batch processing

Press the Start button in the Queue dialog.

You will see a progress bar for the current task and for the whole queue.
You will also see a preview of the first image in the current task. In the report window, the list of processed images is shown.

Completed tasks are removed from the queue.

You can stop processing and close the program at any time. The queue contents will be saved and you will be able to continue processing later.

Please note, that resulting images are also saved in the output list on the Parameters  tab. You can select one of the resulting images there and retouch it. You will not be able to do this after you exit the program!

Helicon Focus is able to generate web pages with animated image stack.

On the Saving tab press Create animation button to open window with additional parameters.

In this window you can define resolution of the images, folder to place animation, title on the web page with animation and comments.

 Align images check box defines if images are aligned or shown without modifications.

 Static resulting image check box defines if resulting image is shown as a static image on the web page or it is included into animation.

 Calculate file size button helps to estimate how much space the animation will take.

Sample images:
Click to see the original files and download the samples.

Updates and support

We support users via email (support@heliconfilter.com) and in the forum (http://forum.helicon.com.ua/). Naturally, registered users are served first.

If you want to be notified about new versions of the program, subscribe to our newsletter at our program home page (heliconsoft-subscribe@googlegroups.com).

Contacts

Web:

• http://www.heliconsoft.com/

Emails:

• support@heliconfilter.com


• DanKozub@helicon.com.ua

Post address:

Helicon Soft Ltd.
per. Mekhanichesky, 4
61068 Kharkov
Ukraine

Tel: +380-67-579-52-44

Copyright

Authors: Danylo Kozub, Vitaly Khmelik, Juri Shapoval, Vitaly Chentsov, Stanislav Yatsenko

Helicon Soft Ltd. (c) 2000-2008
All rights reserved.