Macro Exercises #3 Focus stacking

Lord VetinariLord Vetinari SmugbugPosts: 14,894Registered Users Major grins
edited October 21, 2014 in Holy Macro
Macro tutorial 3
Focus stacking.
Focus stacking can be used to increase the available DOF in a shot. You might want to do this where you just can't get the required DOF no matter what aperture you use, or where you are using fairly open apertures to minimise diffraction softening but want to make up some DOF.
First you need to down load and install Combinezm via this link http://www.hadleyweb.pwp.blueyonder.co.uk/CZM/Manual/Install.htm


Taking pics for a stack.

You need a subject which is not moving whilst taking the photos. I tend to use fixed focus move the camera unti the first part of the subject comes into focus, take a shot but note where the subject is just going OOF. I then move the camera in trying to keep the FOV similar and not rotating the camera until the OOF area in the previous shot just comes into focus. Continue doing this until you have coverd the rquired DOF. If you are using a tripod (perhaps recommended for first goes at this) then do the same thing but use the focus ring to move to the next "slice".
I use combinezm directly after doing RAW conversion on the pics. it is important that the pics used are all exactly the same pixel size.

Below are 3 shot slices I'm going to use for this stack of a damselfly sitting next to it's exuvium (empty shell).
pic1
152129088-L.jpg
Pic 2
152128686-L.jpg
Pic 3
152128707-L.jpg

Run Combinezm and load the files by clicking on File/New.
152128719-M.jpg

And choose the file set using the [CTL] key

152128755-L.jpg

To do the stack click on Macro/ Do Stack

152128783-M.jpg

The programme will then chunter away comparing the shots, aligning then, colour matching them.

152128815-M.jpg

Finding detail, applying low and high pass filters before the stacked image appears.
Use the File/ Save Frame/Picture as Dialogue to name and save the picture. I use quality 100% jpgs.

152128871-L.jpg


You'll notice that in this stacked picture there is some Distortion on the RHS- this is normal and is caused by the slight change in FOV that has to occur in the different slices (ie that part of the image was missing in some of the slices). You just crop this off in PP. However there is also some disappointing noise blotching in the background. You may also see some haloing (not in this example) around high contrast edges. The latter two defects are caused by mis-alignment of the shots. This can sometimes be helped by clicking on Stack/ Reverse order and doing the stack again. However a more precise way of dealing with it, is to align the pictures manually before doing the stack. Doing this will also correct any rotational errors present in the different slices.


Manual Alignment.


Use the View/ Go to frame dialogue

152128908-M.jpg

and if the frames were shot in focus order choose the middle frame as the "master" frame.

152128939-M.jpg

Find two readily identifiable spots which are present in all the images and are fairly widely spaced (you may need to look at the other images using the View frames to check this). Place the mouse cursor over the left point and hit the 1 key and then click on exit in the dialogue box. Place the cursor on the right hand side point and hit the 2 key- click on exit on the resulting dialogue box.

152128976-L.jpg

Now use the View frames dialogue to go to another frame. Place the cursor over the LHS point and hit the 3 key, click on exit in the resulting dialogue box. Place the cursor over the RHS point and hit the 4 key. Now instead of clicking on Exit, click on Set and Use Params then click on OK in the next dialogue box

152129010-M.jpg

152129029-M.jpg

Repeat the latter process on all the remaining slices (not the "master") re-using the 3 and 4 keys.
When you have finished click on Macro/ do Stack again and let it run through

152129606-L.jpg

You'll see this time the image is cleaner- save it and then do a de- noise and clean up the image in PP.
Resulting stacked Image

152128675-L.jpg.

Exercise
Fairly obvious- find a suitable subject and take a slice sequence- use the software to put the image together and then post back here the first shot in the slice set and the resulting stacked image.
Brian Valentine.
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Comments

  • SkippySkippy Forensic Wannabe Posts: 12,075Registered Users Major grins
    edited May 13, 2007

    WOW!!!! clap.gif Now this is the tutorial I am sure many many folks have been keen for you to produce Brian nod.gif

    I've just downloaded CombineZm, and was pleased that VISTA let me load it on my computer :ivar .... but it didn't come with a free bug to try it with hehehe.

    An excellent Tutorial Brian, and I hope folks will show us their results from learning this amazing Stacking Technique.

    Thank you again clap.gif ..... Skippy
    .

    .
    Skippy (Australia) - Moderator of "HOLY MACRO" and "OTHER COOL SHOTS"

    ALBUM http://ozzieskip.smugmug.com/

    :skippy Everyone has the right to be stupid, but some people just abuse the privilege :dgrin
  • AndyAndy Bicameral New YorkPosts: 60,808Registered Users Major grins
    edited May 13, 2007
    clap.gif Brian :D

    May we have your permission to have this live permanently on our Tutes site at http://dgrin.smugmug.com ?
  • Lord VetinariLord Vetinari Smugbug Posts: 14,894Registered Users Major grins
    edited May 14, 2007
    Skippy wrote:

    WOW!!!! clap.gif Now this is the tutorial I am sure many many folks have been keen for you to produce Brian nod.gif

    I've just downloaded CombineZm, and was pleased that VISTA let me load it on my computer :ivar .... but it didn't come with a free bug to try it with hehehe.

    An excellent Tutorial Brian, and I hope folks will show us their results from learning this amazing Stacking Technique.

    Thank you again clap.gif ..... Skippy
    .

    No probs Skippy :)
    You could always try it with my low res slices above, but you would need to ensure the pixel sizes of the 3 pics are exactly the same.

    Brian V.
  • Lord VetinariLord Vetinari Smugbug Posts: 14,894Registered Users Major grins
    edited May 14, 2007
    Andy wrote:
    clap.gif Brian :D

    May we have your permission to have this live permanently on our Tutes site at http://dgrin.smugmug.com ?

    Hi Andy- no problem with that.

    brian V.
  • Phil_LPhil_L Major grins Posts: 106Registered Users Major grins
    edited May 15, 2007
    OK I recently got my Macro back from calibration so Ill break out of lurking mode to try this.

    Some fantastic work beeing shown here. Hardly dare post anything myself.yelrotflmao.gif ne_nau.gif :D

    Done on a tripod indoors. F11, SS ~1 sek with timer. Started at Macro 1:1 and used the focus ring to go further out.

    Havent got round to the focusing tutorial yet, so I didnt dare try hand held.

    First shot:

    152904285-L.jpg

    Stacked 6 shots in total:

    152904617-L.jpg

    Could do with some added "pop" but...

    Havent tried the manual stacking jig yet. Have to do it later since life is making some heavy duty inroads into the fun stuff.

    Impressive software and a really interesting tutorial. :D wings.gif

    Thanks.bowdown.gif bowdown.gif
  • Lord VetinariLord Vetinari Smugbug Posts: 14,894Registered Users Major grins
    edited May 15, 2007
    Excellent stack Phil- can't see anything that needs cleaning up apart from the FOV boundary on the RHS (just needs cropping off). Excellent comparison between the first shot and the stacked result :). You really shouldn't have to do manual alignment on shots taken with a tripod (no rotation and fairly constant FOV)

    Brian V.
  • hgernhardtjrhgernhardtjr Docendo discimus. Posts: 417Registered Users Major grins
    edited May 15, 2007
    Brian, Perhaps you could answer this for me.

    I've used HeliconFocus ( http://www.heliconsoft.com/heliconfocus.html ) for several microscopic shots (and a few macros) in the past that needed to be stacked to enhance the visible DOF but it can be a bit costly (US$30 for one year, $115 for life) if you do not use it much (although I do like its interface). CombineZM is aparently "free". Rather than buy another year's license, do you feel Combine ZM is as good as HeliconFocus Lite?

    When I get some time I will download and play with CombineZM, but was hoping you might be able to give me a quick answer. Thanks for letting me "pick your brain"! Also, EXCELLENT tutorial!!!

    -Henry-
    — Henry —
    Nam et ipsa scientia potestas est.
  • Lord VetinariLord Vetinari Smugbug Posts: 14,894Registered Users Major grins
    edited May 15, 2007
    Brian, Perhaps you could answer this for me.

    I've used HeliconFocus ( http://www.heliconsoft.com/heliconfocus.html ) for several microscopic shots (and a few macros) in the past that needed to be stacked to enhance the visible DOF but it can be a bit costly (US$30 for one year, $115 for life) if you do not use it much (although I do like its interface). CombineZM is aparently "free". Rather than buy another year's license, do you feel Combine ZM is as good as HeliconFocus Lite?

    When I get some time I will download and play with CombineZM, but was hoping you might be able to give me a quick answer. Thanks for letting me "pick your brain"! Also, EXCELLENT tutorial!!!

    -Henry-

    Henry - I do have helicon focus but only tried it after I been using combinezm and I'm still using combinezm. I had more stack errors with helicon- not sure if it's less forgiving of mis-alignments or not but I just found combinezm more reliable in giving reasonable stacks.
    brian V.
  • hgernhardtjrhgernhardtjr Docendo discimus. Posts: 417Registered Users Major grins
    edited May 15, 2007
    Thanks for the input Brian ... I, too, noticed some stack errors and would have to re-do the procedure a couple of times with HeliconFocus ... I'll get CombineZM downloaded and play around with it in some spare time!
    — Henry —
    Nam et ipsa scientia potestas est.
  • wxwaxwxwax Immoderator Posts: 15,471Registered Users Major grins
    edited May 15, 2007
    Awesome software tutorial.
    Sid.
    Catapultam habeo. Nisi pecuniam omnem mihi dabis, ad caput tuum saxum immane mittam
    http://www.mcneel.com/users/jb/foghorn/ill_shut_up.au
  • SkippySkippy Forensic Wannabe Posts: 12,075Registered Users Major grins
    edited May 15, 2007
    Phil_L wrote:
    OK I recently got my Macro back from calibration so Ill break out of lurking mode to try this.
    Some fantastic work beeing shown here. Hardly dare post anything myself.yelrotflmao.gif ne_nau.gif :D

    Done on a tripod indoors. F11, SS ~1 sek with timer. Started at Macro 1:1 and used the focus ring to go further out.
    Havent got round to the focusing tutorial yet, so I didnt dare try hand held.
    First shot:
    Stacked 6 shots in total:
    Could do with some added "pop" but...
    Havent tried the manual stacking jig yet. Have to do it later since life is making some heavy duty inroads into the fun stuff.
    Impressive software and a really interesting tutorial. :D wings.gif

    Thanks.bowdown.gif bowdown.gif

    Hi Phil, it's amazing how much detail is brought out in STACKING.
    Nice to see your not lurking any more :D .

    I'm keen to try this stacking technique out myself, it's a matter of finding something to try it on :D .

    Thanks for sharing your stacked image Phil, hard to believe from the looks of the first image that you could end up with a result as in your second image ... Well Done thumb.gif .... Skippy
    .
    .
    Skippy (Australia) - Moderator of "HOLY MACRO" and "OTHER COOL SHOTS"

    ALBUM http://ozzieskip.smugmug.com/

    :skippy Everyone has the right to be stupid, but some people just abuse the privilege :dgrin
  • tleetlee Perma Grin Posts: 1,090Registered Users Major grins
    edited May 16, 2007
    O.K. Here's my try with the stacking program. Well, I actually used 3 images in the stacking program, then "manually" stacked on two more. Only reason I did 2 manually, is because I noticed I had some blurred areas (that I had not focused on in the 1st 3 stacked images). I am noticing that when I am capturing the images, I am not getting all the details (that I want) in focus--like I think I am. But, practice will make perfect...I hope :D.

    "First" non stacked image:

    153270862-L.jpg



    Stacked Image:

    153270660-L.jpg

    T :D

    www.studioTphotos.com

    "Each day comes bearing its own gifts. Untie the ribbons."
    ----Ruth Ann Schubacker
  • Lord VetinariLord Vetinari Smugbug Posts: 14,894Registered Users Major grins
    edited May 16, 2007
    Again worked very well Tlee :)
    As you say getting the slices you want comes with practice. This is a nice example because you still have some nice OOF areas in the pic which gives a sense of depth. One problem with focus stacking is that it takes away the visual clues we use to judge depth and so if it is done too much you can end up with a very "flat" looking shot.
    Brian V.
  • tleetlee Perma Grin Posts: 1,090Registered Users Major grins
    edited May 16, 2007
    Again worked very well Tlee :)
    As you say getting the slices you want comes with practice. This is a nice example because you still have some nice OOF areas in the pic which gives a sense of depth. One problem with focus stacking is that it takes away the visual clues we use to judge depth and so if it is done too much you can end up with a very "flat" looking shot.
    Brian V.


    Makes sense. Thanks. thumb.gif

    T :D

    www.studioTphotos.com

    "Each day comes bearing its own gifts. Untie the ribbons."
    ----Ruth Ann Schubacker
  • SkippySkippy Forensic Wannabe Posts: 12,075Registered Users Major grins
    edited May 17, 2007
    tlee wrote:
    O.K. Here's my try with the stacking program. Well, I actually used 3 images in the stacking program, then "manually" stacked on two more. Only reason I did 2 manually, is because I noticed I had some blurred areas (that I had not focused on in the 1st 3 stacked images). I am noticing that when I am capturing the images, I am not getting all the details (that I want) in focus--like I think I am. But, practice will make perfect...I hope :D.

    "First" non stacked image:





    Stacked Image:


    Wow you can soooooooo see the difference eek7.gif truly amazing the difference stacking can make clap.gif .
    The more you do the better you will get at it, but gosh it looks great for a first attempt thumb.gif ...... Skippy
    .
    .
    Skippy (Australia) - Moderator of "HOLY MACRO" and "OTHER COOL SHOTS"

    ALBUM http://ozzieskip.smugmug.com/

    :skippy Everyone has the right to be stupid, but some people just abuse the privilege :dgrin
  • ShepsMomShepsMom Gone Crazy, Be Back... Posts: 4,319Registered Users Major grins
    edited May 19, 2007
    This is great, but is there a program like this for a Mac?? ne_nau.gifdunno I would love to try it.
    Marina
    www.intruecolors.com
    Nikon D700 x2/D300
    Nikon 70-200 2.8/50 1.8/85 1.8/14.24 2.8
  • Lord VetinariLord Vetinari Smugbug Posts: 14,894Registered Users Major grins
    edited May 20, 2007
    ShepsMom wrote:
    This is great, but is there a program like this for a Mac?? ne_nau.gifdunno I would love to try it.
    Hi Marina
    Only progs for a MAC I've seen are Helicon focus (commercial but with 30Day free trial) or this http://bigwww.epfl.ch/demo/edf/ which I think is freeware plugin for another freeware prog (imagej?)

    Brian V.
  • mwaltersmwalters Major grins Posts: 119Registered Users Major grins
    edited May 21, 2007
    Hello!

    This is my first effort with stacked images - 12 in total, then a bit of post to remove a few bits of sensor grime.

    My wife keeps asking for a stack of lillies...

    154902509-L.jpg

    154900254-L.jpg

    At least flowers don't run away as I'm trying to focus. I tried to follow a bee yesterday!

    Matthew

    (Great tutorial, thanks. I had tried CombineZM before but lack of will power beat me.)
  • Lord VetinariLord Vetinari Smugbug Posts: 14,894Registered Users Major grins
    edited May 21, 2007
    That's quite a stack Mathew- and it worked very well- Lilly petals always look like alien landscapes to me :)
    Brian V.
  • mwaltersmwalters Major grins Posts: 119Registered Users Major grins
    edited May 21, 2007
    That's quite a stack Mathew- and it worked very well- Lilly petals always look like alien landscapes to me :)
    Brian V.

    They do have a great texture. I guess I got carried away watching the focus move on the water droplets!

    Matthew
  • SkippySkippy Forensic Wannabe Posts: 12,075Registered Users Major grins
    edited May 21, 2007
    mwalters wrote:
    Hello!

    This is my first effort with stacked images - 12 in total, then a bit of post to remove a few bits of sensor grime.
    My wife keeps asking for a stack of lillies...
    At least flowers don't run away as I'm trying to focus. I tried to follow a bee yesterday!

    Matthew
    (Great tutorial, thanks. I had tried CombineZM before but lack of will power beat me.)

    Hi Matthew, you can clearly see the difference in your two shots thumb.gif
    Well Done clap.gif .... Skippy
    .
    .
    Skippy (Australia) - Moderator of "HOLY MACRO" and "OTHER COOL SHOTS"

    ALBUM http://ozzieskip.smugmug.com/

    :skippy Everyone has the right to be stupid, but some people just abuse the privilege :dgrin
  • Lord VetinariLord Vetinari Smugbug Posts: 14,894Registered Users Major grins
    edited May 26, 2007
    Thought I'd add a recent one of mine.

    Just a 2 shot stack

    Brian V.

    156396388-L.jpg

    156396338-L.jpg
  • Antonio CorreiaAntonio Correia Always learning Setubal - PortugalPosts: 6,181Registered Users Major grins
    edited May 26, 2007
    :jawdrop
    :Dthumb.gif
    All the best ! ... António Correia - Facebook
  • SkippySkippy Forensic Wannabe Posts: 12,075Registered Users Major grins
    edited May 27, 2007
    Almost got it right Brian rolleyes1.gif
    It's not as easy to see the stages at all as I thought it would be,
    maybe its the subject I chose?

    Here's my attempt, I can see it has a flaw in it, but I do see how it all comes together now, so I'm happy with that :D
    .... Skippy
    .


    Here is the Final Image, faulty but not too bad :D

    156569936-L.jpg
    .
    Below is one of the images used in the Stack
    .
    .
    Skippy (Australia) - Moderator of "HOLY MACRO" and "OTHER COOL SHOTS"

    ALBUM http://ozzieskip.smugmug.com/

    :skippy Everyone has the right to be stupid, but some people just abuse the privilege :dgrin
  • Lord VetinariLord Vetinari Smugbug Posts: 14,894Registered Users Major grins
    edited May 27, 2007
    Skippy wrote:
    Almost got it right Brian rolleyes1.gif
    It's not as easy to see the stages at all as I thought it would be,
    maybe its the subject I chose?

    Here's my attempt, I can see it has a flaw in it, but I do see how it all comes together now, so I'm happy with that :D
    .... Skippy

    .

    Hi skippy- Beautiful Lilly
    the stack looks as if it has worked perfectly- you always get a border somewhere caused by the FOVs changing- you just crop that off (on the RHS)- the image output from the stacking prog is actually bigger than the input sizes so you are not really cropping :)
  • SkippySkippy Forensic Wannabe Posts: 12,075Registered Users Major grins
    edited May 27, 2007
    Hi skippy- Beautiful Lilly
    the stack looks as if it has worked perfectly- you always get a border somewhere caused by the FOVs changing- you just crop that off (on the RHS)- the image output from the stacking prog is actually bigger than the input sizes so you are not really cropping :)

    Ohhhhhhh good, thanks Brian :D
    I tell you folks if I can do it, you can do it nod.gif

    Thanks for the wonderful tutorial, I need to find meself a bug now thumb.gif
    ... Skippy
    .
    .
    Skippy (Australia) - Moderator of "HOLY MACRO" and "OTHER COOL SHOTS"

    ALBUM http://ozzieskip.smugmug.com/

    :skippy Everyone has the right to be stupid, but some people just abuse the privilege :dgrin
  • zinizini Big grins Posts: 37Registered Users Big grins
    edited May 30, 2007
    stacking -
    ne_nau.gifwho knew I sure didn't bowdown.gifbowbowdown.gifbowbowdown.gifbow great tutorial, can this be done in CS2?

    I cannot wait to try this. I am with skippy I am going bug hunting!
  • Lord VetinariLord Vetinari Smugbug Posts: 14,894Registered Users Major grins
    edited May 30, 2007
    zini wrote:
    ne_nau.gifwho knew I sure didn't bowdown.gifbowbowdown.gifbowbowdown.gifbow great tutorial, can this be done in CS2?

    I cannot wait to try this. I am with skippy I am going bug hunting!
    Well it can be done in PS but is much harder. The programme combinezm is freeware - much easier to use that.
    Brian V.
  • SkippySkippy Forensic Wannabe Posts: 12,075Registered Users Major grins
    edited June 11, 2007
    ... Test .. Skippy
    .
    .
    Skippy (Australia) - Moderator of "HOLY MACRO" and "OTHER COOL SHOTS"

    ALBUM http://ozzieskip.smugmug.com/

    :skippy Everyone has the right to be stupid, but some people just abuse the privilege :dgrin
  • Lord VetinariLord Vetinari Smugbug Posts: 14,894Registered Users Major grins
    edited June 11, 2007
    Skippy wrote:
    ... Test .. Skippy
    .
    What you testing for ? - ah not a sticky now ? ?

    Brian V.
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