New, easy to use stacking software

[Bruce Williams]

I thought some of you might be interested to hear about my recent experience using a fairly new (and FREE) image stacking program called Zerene Stacker (ZS).

I've been using image stacking software for about 3 years now (mainly using CombineZP and earlier releases). I use it to stack images taken through my stereo microscope and when shooting close-up and macro on the bench (mostly finely detailed fossils) and in the field (insects and spiders).

About 6 weeks ago I was contacted by the developer (Rik Littlefield) suggesting I might like to try out ZS. He was particularly interested to see how the product worked out in the field where alignment of the individual frames would typically not be as precise. Rik calls the process of shooting and stacking hand-held images in the field "Wild Stacking". An appropriate and quite fun term for it I think .

I know that several WAB members are experienced "stackers" however for the benefit of readers that may not be familiar with technique here's a brief explanation of the what and why of Image Stacking:

A major problem with macro photography is that at high magnification the depth of field becomes very shallow. In practical terms this means that at typical macro lens magnification of 1:1 only a part of even a very small subject will be sharply in focus. Take a look at the following four images of a barklouse that measured ~3.5mm long (when viewed side-on). You can clearly see that only a part of each image is sharply in focus.



Stacking software compares (in this instance) the four images. First it aligns each image and then combines the sharpest (most in focus) bits from each of the four images to produce a single stacked (highly detailed) image. This is the result of stacking the above 4 images using ZS:



You can stack any number of images from just 2 to well over 100 (table top macro). Typically I take between 2 and 6 images when stacking in the field (wild stacking). By way of comparison I generally take between 40 and 50 frames when shooting a 3mm deep fossil slab through my Mieji stereo microscope.

Continued.....see next entry (forum would not accept as a single post?)

Bruce

[Bruce Williams]

Continued.......from original post

For anyone that's interested:

When photographing frames to stack (like the above example) I shoot entirely manually. That means manually controlled pop-up flash at around 1/250s at f/14. I hand-hold all my shots, leaning on whatever is handy. I'm not steady enough to shoot frames for stacking if there's nothing to lean against (a fence, a tree or as last resort a stick).

I quickly decide (using experience) on how many frames I think I'll need to cover my subject from front to back (2 - 6 shots). Next I focus and shoot the nearest part of the subject (frame 1). For wild stacking I prefer to move the camera rather than use the lens focus ring, so I move the camera into the subject pressing the shutter as the selected bit of anatomy pops into focus (frame 2). I repeat until I've shot all the frames (frames 3+).

The amount of movement between frames is tiny and I find the easiest way of controlling the point of focus is to press my eye into the eyepiece and allow the camera to gradually move forward against the resistance of the hand holding the camera.

I always shoot front to back in case the subject decides to move or do a runner mid way through. The nearest couple of frames generally make an acceptable image (see the example 4 frames in this post) so I know at least I'll have something worthwhile.

Prior to using ZS (or CombineZP) I check the frames in Photoshop by loading them all into different layers and flicking between them. If alignment is poor then I manually rotate and roughly align all the images and use "Save as" to create a set that I'm confident will stack ok. This process isn't always necessary and when it is, it usually takes far less time than one might imagine.

Finally, I have compared results of Zerene Stacker with CombineZP (using from 2 to 6 frames) and to be honest there is very little difference in performance. However ZS is VERY easy to use - just drag in your frames and select Align and Stack from the menu - and you're done. ZS also offers an alternative stacking method for subjects with a lot of overlapping hairs or bristles (or stamens in the case of flowers).

Bruce

[Words]

Bruce, that's a really helpful run through of how you do this. I used to play around with CombineZP, but needed to reinstall on a new machine anyway as my old PC packed up. Will give this a go.

[squishy]

i've used combine ZM when i've needed to. i'll look into ZS

[acherontia]

What an interesting and helpful post - it more or less covers everything that my OH has been mulling over re stacking in detailed macro work - especially those in the studio done with bellows .

He says 'Ta very much!' (he's a scouser )

Invaluable information re the free ZS too! Cheers.

Acherontia

[Geoff F]

I downloaded the Combine ZP previously but I couldn't get it to run successfully. After my computer had been running for over an hour on a simple 4 frame stack I decided that ZP was short for ZAP; which is what I did with that programme.

But I will have a look at this alternative.

[Bruce Williams]

Thanks for your comments folks - I'm glad you found the info of interest.

I should mention that I experienced an initial problem getting the software to run. I got a message telling me that the Java Virtual Machine failed to launch. This is a known problem and there is an easy workaround. This page covers all know issues: Zerene Stacker Known Issues

Geoff - Your problem sounds like it could be memory related. If you're running with 1Gb or less of RAM you may have to reduce your image size (not file size) before stacking. Cropping is best of course but if you experience problems and you can't crop it may also be worth trying to resample down to a smaller image format (but keep it as large as you can of course).

Bruce

Bruce

[Bruce Williams]

I forgot to mention....

One very useful feature offered by Zerene Stacker is the ability to retouch a stacked image to correct the typical stacking errors made by all stacking software. This feature is probably best understood by watching this video tutorial: Zerene Stacker Retouching

Bruce

[acherontia]

Bruce - I've uploaded my version successfully (haven't tried it yet) but OH who has a MAC has no tool bar appearing on his so can't try it out! He's got an iMac 5.

Acherontia

[Bruce Williams]

Hi acherontia,

The software runs under Windows and Macintosh OS X. I suggest your OH drop an email to support@zerenesystems.com describing the problem. I'm sure he'll get a quick and helpful response.

Bruce

[Bruce Williams]

Btw - if you're planning to give ZS a try take a quick look at this one-page "Getting Started" tutorial. I found it quite helpful.

Bruce

[Jethro Tull]

Originally Posted by Bruce Williams

I thought some of you might be interested to hear about my recent experience using a fairly new (and FREE) image stacking program called Zerene Stacker (ZS).

I've been using image stacking software for about 3 years now (mainly using CombineZP and earlier releases). I use it to stack images taken through my stereo microscope and when shooting close-up and macro on the bench (mostly finely detailed fossils) and in the field (insects and spiders).

About 6 weeks ago I was contacted by the developer (Rik Littlefield) suggesting I might like to try out ZS. He was particularly interested to see how the product worked out in the field where alignment of the individual frames would typically not be as precise. Rik calls the process of shooting and stacking hand-held images in the field "Wild Stacking". An appropriate and quite fun term for it I think .

I know that several WAB members are experienced "stackers" however for the benefit of readers that may not be familiar with technique here's a brief explanation of the what and why of Image Stacking:

A major problem with macro photography is that at high magnification the depth of field becomes very shallow. In practical terms this means that at typical macro lens magnification of 1:1 only a part of even a very small subject will be sharply in focus. Take a look at the following four images of a barklouse that measured ~3.5mm long (when viewed side-on). You can clearly see that only a part of each image is sharply in focus.



Stacking software compares (in this instance) the four images. First it aligns each image and then combines the sharpest (most in focus) bits from each of the four images to produce a single stacked (highly detailed) image. This is the result of stacking the above 4 images using ZS:



You can stack any number of images from just 2 to well over 100 (table top macro). Typically I take between 2 and 6 images when stacking in the field (wild stacking). By way of comparison I generally take between 40 and 50 frames when shooting a 3mm deep fossil slab through my Mieji stereo microscope.

Continued.....see next entry (forum would not accept as a single post?)

Bruce

Brilliant shot Bruce! what lens do you use for Macro? I have a Canon 1Dmk2 and plenty big lenses but fancy getting a macro
Cheers
Brian

[Bruce Williams]

Thanks Brian .

I use a Nikon 105mm VR Macro lens on a Nikon D300 so unfortunately not an option for your 1D MkII. However I know a lot of members use Sigma lenses and have been very pleased with their results.

The main consideration is probably which focal length to opt for. With Sigma the options are (I believe) 70mm, 105mm, 150mm or 180mm. They all offer ~1:1 magnification so probably the most important difference is working distance and cost. Essentially the longer the focal length the greater the working distance (an advantage with skittish insects). On the other hand the longer focal length lenses are heavier and they cost considerably more.

Your 1D MkII sensor is full frame so will influence the compatibility and performance of a macro lens with DX coverage. Maybe it would be worthwhile geting recommendations and info by posting a new forum thread.

There was a recent forum thread asking for recommendations for a macro lens that you might find interesting: what macro lens??

Bruce

[wildlifesnapper]

Hi,

thanks for the info Bruce. Your results look great.It's something I've never tried so I've downloaded the software and look forward to having a play

neil

[Bruce Williams]

Thanks Neil - I'm sure you'll be pleased with the results.

You might be interested to see this 4 image stack of a Harlequin Ladybird nymph I did using Zerene Stacker today:



Bruce

ps - I forgot to include the promised link to the ZS "How to Use" web page mentioned in an earlier post of mine: Zerene Stacker -- How to Use It

[Ed Tyler]

Thanks for the info and examples Bruce.

I don't own a macro lense, instead I use a set of extension tubes and this is one of my biggest frustrations, so thank you for showing a possible solution to the problem.

Ed

[squishy]

larva, not nymph, Bruce


i've downloaded it, and it is very good! unfortunately, alot of subjects don't stay still enough to take images for stacking

[Bruce Williams]

Thanks Ed.

I hope stacking proves helpful to you. It does take a bit of experimentation to work out an appropriate step size (movement between each frame). It's important not to allow too large a step else you'll end up with out-of-focus bands at various depths through the image.

Adam,

You're dead right there Adam . However fortunately quite a few do and sooner or later even one of the most skittish species will hold still long enough for you to take the 2 to 6 shots necessary to get your stack. I'm repeating myself here, but that's why I always start with the nearest (most interesting) part of the subject, as even if you only get the first shot off before the subject moves or disappears it's often worth keeping - and the odds of getting a keeper improve with each focus step.

I frequently plan for 4 shots but only get 2 or 3 before my subject moves. More often than not even 2 frames are worth stacking and you get more dof than with the single shot. I reckon it takes me about 5 secs to recompose for each frame so with 4 frames that's 15 secs that the subject needs to stay still from the moment I fire the first shot.

Another advantage of stacking is that you can afford to use a slightly wider aperture. While this means shallower dof per frame it generally means better IQ as there is less softness due to the diffraction limitation effect. With my D300 + Nikon 105mm Macro lens I usually shoot single images (no plans to stack) at an effective aperture of f/16 - f/18 whereas when I shoot stacking frames I set the aperture between f/11 - f/14.

Bruce

[squishy]

i can't go any smaller than F/11, and to get that i have to use full manual, because, for some reason, aperture priority only lets me down to F/8

[glsammy]

Some helpful info here Bruce, thanks.

I've used the Combine software before, but not recently. I struggle trying to stack images taken with my MP-e65mm, simply because the lens doesn't focus! The only way you can focus with that lens is to move the lens either closer or further from the subject, which makes stacking very difficult. If anyone has used that lens and has successfully stacked images, I'd be very pleased to hear how you managed it.
I'll try that this software and give it a go.

[Bruce Williams]

Cheers Graham .

Interestingly all my in the field shooting (for stacking) has been done by moving the camera rather than using the lens' focus ring. In the past I have tried using the focus ring but I found it tended to induce unwanted rotation and generally more image displacement. Stacking software does handle this but I feel (intuitive not scientific ) that stacking is more likely to be successful if the images are coincident in the frame.

As I've said all my shooting in the field is hand-held. However I've not hand-held for stacking with anything like the magnification possible with your MP-e65 lens. I've done a small amount of hand-held stacking (with very tiny subjects) using 68mm of extension tube on my 105mm macro lens (approx 2:1). My approach there is to shoot as many frames as I can (before subject moves) and select the ones (2 or 3 at most) that will extend my dof.

I also do a fair bit of table top macro work with MUCH larger stacks. In this case I always use the focus ring as I don't own a focussing rack.

Graham, I'm sure you'll find Zerene's powerful retouching facility to be a major benefit with field based stacking, Here's a link to the tutorial: Zerene Stacker Retouching

Bruce

[glsammy]

I'll just have to try again then Bruce.
The problem I get is the changing image size by focusing on a different area, I can never seem to get the registration right.
I must admit I haven't been trying too hard recently, I think a bit more effort from me might be what's needed.
I've already watched the video link, thanks. How on earth they managed to get that many stacks is beyond me, unless they used a dead insect!
Just goes to show it's a lack of effort on my part rather than any other real problem.