Macro Exercises #3 Focus stacking

Lord Vetinari · May-13-2007, 05:35 AM

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....al/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

Pic 2

Pic 3

Run Combinezm and load the files by clicking on File/New.

And choose the file set using the [CTL] key

To do the stack click on Macro/ Do Stack

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

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.

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

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

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.

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

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

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

.

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.

**Skippy** · May-13-2007, 02:49 PM

WOW!!!!

Now this is the tutorial I am sure many many folks have been keen for you to produce Brian

I've just downloaded CombineZm, and was pleased that VISTA let me load it on my computer

.... 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

..... Skippy
.

***Andy*** · May-13-2007, 04:35 PM

Brian

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

Lord Vetinari · May-13-2007, 09:28 PM

Quote:

Originally Posted by Skippy

WOW!!!!

Now this is the tutorial I am sure many many folks have been keen for you to produce Brian

I've just downloaded CombineZm, and was pleased that VISTA let me load it on my computer

.... 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

..... 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 Vetinari · May-13-2007, 09:28 PM

Quote:

Originally Posted by Andy

Brian

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_L · May-15-2007, 05:11 AM

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.

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.

Thanks.

Lord Vetinari · May-15-2007, 06:48 AM

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.

hgernhardtjr · May-15-2007, 07:46 AM

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-

Lord Vetinari · May-15-2007, 07:52 AM

Quote:

Originally Posted by hgernhardtjr

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.

hgernhardtjr · May-15-2007, 08:13 AM

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!

**wxwax** · May-15-2007, 10:05 AM

Awesome software tutorial.

**Skippy** · May-15-2007, 02:51 PM

Quote:

Originally Posted by Phil_L

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.

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.

Thanks.

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

.

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

.

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

.... Skippy
.

tlee · May-16-2007, 08:03 AM

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

.

"First" non stacked image:

Stacked Image:

Lord Vetinari · May-16-2007, 09:39 AM

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.

tlee · May-16-2007, 03:29 PM

Quote:

Originally Posted by Lord Vetinari

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.

**Skippy** · May-17-2007, 03:24 AM

Quote:

Originally Posted by tlee

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

.

"First" non stacked image:

Stacked Image:

Wow you can soooooooo see the difference

truly amazing the difference stacking can make

.
The more you do the better you will get at it, but gosh it looks great for a first attempt

...... Skippy
.

ShepsMom · May-19-2007, 12:41 PM

This is great, but is there a program like this for a Mac??

I would love to try it.

Lord Vetinari · May-19-2007, 10:14 PM

Quote:

Originally Posted by ShepsMom

This is great, but is there a program like this for a Mac??

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.

mwalters · May-21-2007, 11:29 AM

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.)

Lord Vetinari · May-21-2007, 12:56 PM

That's quite a stack Mathew- and it worked very well- Lilly petals always look like alien landscapes to me :)
Brian V.

May-13-2007, 05:35 AM	#1
Lord Vetinari Smugbug Join Date: Jun 2005 Posts: 6,776	Macro Exercises #3 Focus stacking 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....al/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 Pic 2 Pic 3 Run Combinezm and load the files by clicking on File/New. And choose the file set using the [CTL] key To do the stack click on Macro/ Do Stack The programme will then chunter away comparing the shots, aligning then, colour matching them. 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. 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 and if the frames were shot in focus order choose the middle frame as the "master" frame. 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. 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 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 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 . 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. __________________ Brian V. http://www.flickr.com/photos/lordv/ http://www.lordv.smugmug.com/ Last edited by Lord Vetinari; May-13-2007 at 09:33 PM.

May-13-2007, 02:49 PM	#2
Skippy Forensic Wannabe Join Date: Jan 2004 Location: Geelong Victoria Australia Posts: 12,069	WOW!!!! Now this is the tutorial I am sure many many folks have been keen for you to produce Brian I've just downloaded CombineZm, and was pleased that VISTA let me load it on my computer .... 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 ..... Skippy . __________________ . Skippy (Australia) - Moderator of "HOLY MACRO" and "OTHER COOL SHOTS" ALBUM http://ozzieskip.smugmug.com/ Everyone has the right to be stupid, but some people just abuse the privilege

May-15-2007, 06:48 AM	#7
Lord Vetinari Smugbug Join Date: Jun 2005 Posts: 6,776	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. __________________ Brian V. http://www.flickr.com/photos/lordv/ http://www.lordv.smugmug.com/

May-15-2007, 10:05 AM	#11
wxwax Immoderator Join Date: Dec 2003 Location: Atlanta, GA Posts: 15,442	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

May-16-2007, 08:03 AM	#13
tlee Perma Grin Join Date: Oct 2006 Posts: 1,090	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 . "First" non stacked image: Stacked Image: __________________ -----T www.studioTphotos.com "Each day comes bearing its own gifts. Untie the ribbons." ----Ruth Ann Schubacker

May-13-2007, 04:35 PM	#3
*Andy* SmugMug COO & House Pro Join Date: Dec 2003 Location: New York City Posts: 52,199	Brian May we have your permission to have this live permanently on our Tutes site at http://dgrin.smugmug.com ? __________________ Andy Moon River Photography • Twitter • Facebook

May-15-2007, 05:11 AM	#6
Phil_L Major grins Join Date: Mar 2007 Posts: 106	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. 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. Thanks.

May-15-2007, 07:46 AM	#8
hgernhardtjr Docendo discimus. Join Date: Feb 2005 Location: Parkersburg,WV Posts: 341	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-

May-15-2007, 08:13 AM	#10
hgernhardtjr Docendo discimus. Join Date: Feb 2005 Location: Parkersburg,WV Posts: 341	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!

May-16-2007, 09:39 AM	#14
Lord Vetinari Smugbug Join Date: Jun 2005 Posts: 6,776	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. __________________ Brian V. http://www.flickr.com/photos/lordv/ http://www.lordv.smugmug.com/

May-19-2007, 12:41 PM	#17
ShepsMom Gone Crazy, Be Back... Join Date: Jan 2007 Location: Swamps of Florida Posts: 4,122	This is great, but is there a program like this for a Mac?? I would love to try it. __________________ Marina www.intruecolors.com My Gear: Nikon D80/Nikon D300 18-200mm f/3.5-5.6 G ED-IF AF-S VR DX Nikkor 50mm f/1.8D AF Nikkor 17-55mm f/2.8G SB-600 SB-800

May-21-2007, 11:29 AM	#19
mwalters Major grins Join Date: Jan 2007 Location: Redditch, UK Posts: 119	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.) Last edited by mwalters; May-21-2007 at 12:34 PM.

May-21-2007, 12:56 PM	#20
Lord Vetinari Smugbug Join Date: Jun 2005 Posts: 6,776	That's quite a stack Mathew- and it worked very well- Lilly petals always look like alien landscapes to me :) Brian V. __________________ Brian V. http://www.flickr.com/photos/lordv/ http://www.lordv.smugmug.com/

Thread Tools
Show Printable Version Email this Page
Display Modes
Linear Mode Switch to Hybrid Mode Switch to Threaded Mode