Focus Stacking does not work

[Light_In]

I tried to find a CS6 forum in which I could post but could not find a forum that I was alowed to post in, so forgive me for coming here.

I have taken several photos with multiple focal points and I am trying to merge them in Photoshop CS6 but in every attempt I end up with a single layer that is used while the others indicate no selections at all.

Even when using just 2 images the process only uses the first image and it sets the mask to transparent.

Here are the steps I've been following:

1. Open each of the images I want to stack.
2. Use the Photomerge tool with Auto, Blend Images Together, and Add Open Files. This successfully creates a new image with multiple layers but areas are being selected.
3. Use Auto Blend Layers, Stack Image with Seamless Tones and Colors checked.

The obvious result is no change because only the first layer is being used.

What am I missing?

Tom

[Noel Carboni · Accepted solution]

I'd suggest using the File - Scripts - Load Files into Stack feature rather than Photomerge, as it's more directly what you're wanting to do.

Do your images have a lot of noise in them that could be misinterpreted by the stacking process as detail?

-Noel

[Noel Carboni]

By the way, I just completed a focus stacking operation (starting with Load Files into Stack, then Auto Blend Layers) with 3 small test images and it seemed to work flawlessly:

-Noel

[droblesphoto]

Ive tried every method explained on here to focus stack some images and the result is the where all masks are completely black except for the first one. Ive focused stacked before in CS6 with no problem but CC seems to not work. Ive tried taking other simpler stacked images and results are the same.

Help Please!

[Jeff Arola]

If you have photoshop cc 2014.1, then there is a known bug and adobe says they will fix it in the next update, due out soon.

Photoshop: Auto Blend Layers not focus blending - Photoshop 2014.1

[Light_In]

Noel, after looking through several (CS5) tutorials I found one that used the Load Files into a Stack function.

This worked very well.

No, it had nothing to do with the noise level.

I have tried the process with several images including 3 downloaded files that were used in one of the tutorials. The process fails on both my home PC and my travel laptop.

It never selects any part of any of the layers. The result is that the only thing that remains visible is the first layer.

[AnnShelbourne]

It seems as if Photomerge when used for Focus Stacking is partially broken in CS6.

If I select images in Bridge and use Tools/Photoshop/ Photomerge, I do get a stack of Layers but the images do NOT auto-align.

However, if I choose Bridge/Tools/Photoshop/Load Files into Photoshop Layers;

then, in Photoshop: use Auto Align followed by Auto Blend, I do get a Stack with appropriate Masking.

Photomerge seems to be missing the AutoBlend Layers Panel and the  "Blend Method/Stack Images" checkbox which you get when you do the Stacking in Photoshop one step at a time.

[Light_In]

CameraAnn,

Yes, this is EXACTLY what is happening.

Thank you for including the pictorial reference!

As indicated above, I learned this process from online tutorials that seem to work flawlessly in both CS4 and CS5.

Adobe, if you are watching this thread, you have a bug to fix.

[Noel Carboni]

I don't doubt you're seeing problems but my having made the process work says that it's not a simple bug.  Can you put up some small copies of the images with which the problem can be reproduced?

-Noel

[AnnShelbourne]

I have posted it as a Bug on the Community/Photoshop Family Forum/Problems list as we no longer seem to have access to the formal Bug-reporting forms which general Users used to use for reporting Photoshop Bugs.

There is so much "noise" in that Community area though that i wonder if Bug Reports even get noticed now.

[Noel Carboni]

I'd like to try to reproduce it.  So far it just seems to work for me.

CameraAnn, correct me if I'm wrong but per your screen grab, it seems to work for you too, no?  How did you write it up as a bug if you did not reproduce it?

-Noel

[SG...]

Hi,

I'm not directly involved with this workflow, but if you see tutorials that suggest using Photomerge then it looks like you want to make sure the 'Blend Images Together' option is off in the Photomerge dialog. This will import the images in as layers without the masks (appears to work the same as Ps CS5). Now you'll need to select all the layers and first run Edit> Auto-Align Layers... then run Edit> Auto-Blend Layers...

I'll check with the developer to find if there's a reason the workflow from Bridge doesn't include an alignment option.

regards,

steve

[AnnShelbourne]

Steve:

Thank you for picking-up on this issue.

I have just checked it on CS 5.1 and Photomerge did not work for Focus Stacking in 5.1 either (regardless of whether AutoAlign is checked or not).

I hadn't realised that this issue existed until now because I have always either used the "Load files to Photoshop Layers" option or I use the third party ZereneStacker software for stacking because of its rather powerful editing capabilities.

[Trevor.Dennis]

I have just tried and it worked fine for me.  I generally start by Loading to Layers from Bridge though, and then use Edit > Auto align, and Edit > Aut blend.

[AnnShelbourne]

That is exactly the point:

Focus stacking works if you Load to Photoshop Layers" from Bridge.

Focus stacking does NOT work if you try to use PhotoMerge from Bridge instead.

Perhaps "Photomerge" and "Load Files to Photoshop Layers"  need to be combined as one command because their functions overlap somewhat already but I am sure that having two similar tools must confuse many Users.

While you can make Panos as well as Focus Stacks using "Load Files to Photoshop Layers", it does not seem to make such well aligned Panos as Photomerge does but Photomerge doesn't make Focus Stacks.

This screen shot  shows two Panos made from CS6 using the same set of individual files.

The top Pano was made using "Load Files to Photoshop Layers"; the lower image was made using Photomerge. These examples are shown "as merged" with no further editing or clean-up.

[Trevor.Dennis]

I had an experience with CS5 a while back where Photomerge would not work.  I started the process, but almost imediately stalled and left me with photoshop still on screen, but with no files open.  I was unable to fix it, and this was a fairly newly built system where it had been working fine.  I found that Loading to layers, Align and Merge worked OK, and with results nearer to Ann's second example above, than the first.  Then the CS6 beta came along, and all was well again.

[Noel Carboni]

CameraAnn wrote:

While you can make Panos as well as Focus Stacks using "Load Files to Photoshop Layers", it does not seem to make such well aligned Panos as Photomerge does but Photomerge doesn't make Focus Stacks.

To my mind this is akin to using a hammer vs. a heavy wrench to drive a nail.  Sure, it's possible to do with each, but one is the right tool for the job.  No matter how many people tell you a wrench can be used that way, or who write on the Internet that their old wrench has always worked for it, it's still not the right tool!

Is this continuing to be discussed because there's a lack of an direct way to load images into a stack + auto align by starting in Bridge?  As Trevor mentioned, it seems pretty straightforward to do the individual steps (Edit - Auto align then Edit - Auto blend), and I'll wager it's faster than trying to run through Photomerge.

-Noel

[AnnShelbourne]

My point is that Bridge offers two similar but different tools and I think that it would be a lot less confusing to the Users if these two tools were reconfigured and combined into a single tool which offered appropriate Option buttons and check boxes to  Stack, Align and Blend the Photoshop Layers into either a Focus Stack or a Pano in the most optimal way.

Regretably, CS6 still has no PDF Manual nearly two months after shipping and the fact that this topic was posted in the first place is a clear indication of just how confusing the choice between these two Bridge tools can be.

[Noel Carboni]

I have to respectfully disagree.  Photoshop Elements is the Big Button version that combines bunches of things into hand-holding functions.  Photoshop full version is the professional product that gives us the tools to combine in whatever ways we want.

Regarding the manual...  To be fair they have 4 more days before they miss their goal of publishing the PDF in June. 

-Noel

[AnnShelbourne]

Well the current set-up was confusing enough for people to have used incorrect methods to write and publish Tutorials on the Internet and to have caused Tommy Guns difficulties in making Focus Stacking work.

Regardless of whether or not Photoshop is a "Pro application", there is no reason not to streamline procedures for greater efficiency and ease of use whenever possible and I believe that this is one such instance of where an improvement would be desirable. Even having Tool Tips in Bridge for these items might have helped.

Apart from anything else, how many of the independent books on Photoshop discuss the techniques of Focus Stacking, Stepping Motors, and advanced layer editing at all?

I know that I had to work out a system for myself by trial and error.

Quite by chance, I have just received an e-mail  asking for help on this issue and referencing the very image which I used to test the two procedures in this thread  (which is admittedly rather an extreme case because the image in question is a seed inside a blueberry, shot through a microscope objective with a DOF of .025 mm at 9x life-size on the sensor!).

[SG...]

Hi Ann,

Short story is that Photomerge is a very different use case than Focus Stacking. The first aligns and blends to make a larger image from semi-overlapping images, while the second aligns and blends to make a similar sized image from (ideally) wholly overlapping images.

Photomerge in Photoshop (Ps) [and extended to Bridge] was implemented a version or more before HDR and other image stacking features were implemented. It was originally devloped for making panoramic images. To collapse that workflow into the HDR, Focus Stacking, or Statistics features would be counter productive for more users than it would help. It would  also break compatibility with existing actions and scripts that expect things to be a particular way.

It's unfortunate that there are existing works that try to use the Photomerge workflow for Focus Stacking. My guess is these came from pioneers hacking the Photomerge feature before Ps had support for Focus Stacking. As you've found, it can cause confusion. Using Bridge, you'll want to use "Load Files to Photoshop Layers" or the "Stack-A-Matic" scripts, align if needed, and then run the Auto-Blend... Stack Images workflow. Using Ps, you'll want to use the "Load File into Stacks..." script, again align if needed, and then run the Auto-Blend...Stack Images workflow.

Here's a nice concise and historical look at Focus Stacking: http://www.aravind.ca/Tutorials?edof_cs4

regards,

steve

[AnnShelbourne]

Steve:

Thank you for taking the trouble to find this info..

Possibly one way to deal with the current confusion would be to either add Tool Tips in Bridge and/or change the labelling in the Tools menu.

Perhaps

"Photomerge (Panorama) …"

and

"Load to Photoshop Layers (Stacking) …"

would make the difference clearer to newer Users?

[Noel Carboni]

CameraAnn wrote:

I had to work out a system for myself by trial and error.

If you waited for everything to be done for you, you wouldn't be a pioneer, now would you? 

It's not been too many years since every frame shot cost money.  Just a little over a decade later now we're crying because the process of taking a whole spate of slightly differently-focused images isn't nailed down to a "set it and forget it" process.

It hasn't been too many years since astrophotographers figured out that video cameras can take a whole lot (hundreds or thousands) of frames of the same subject and software could combine pixels to average out noise, and pick and choose frames spoiled by air currents to throw out - and now we have amateur lunar and planetary photography that rivals pro mega-funded observatory stuff.

By the way, Ann, I think I mentioned above - there IS a fully automated solution (maybe not for your microscope, but certainly for lens-based photography) out there - look up Helicon Focus.

-Noel

[AnnShelbourne]

I tested both Helicon Focus and ZereneStacker quite extensively and eventually chose Zerene because  it permits such precise selective editing of each "slice" of the image.

I bought a StackShot stepping motor and this set-up often makes 70 frames (or more!) to build a suitable stack from these microscopic subjects so I was also influenced by the fact that the StackShot company and Zerene work quite closely together.

I am not actually shooting through a microscope but I am using a Microscope lens (objective) on the front of a bellows + cone on a Nikon with the whole rig mounted on the digitally-controlled StackShot.

A real Heath-Robinson monster of a machine if ever there was!

[Noel Carboni]

Cool stuff!  No doubt you can make things with the thing that very few others can.  But probably does not have such mass-market appeal as to make products to support it plentiful.

A friend of mine has worked out how to shoot thorough a fairly expensive microscope and step the focus, then he focus-stacks with the Helicon software.  He occasionally sends me 100+ megapixel photos of whole butterflies where the scales are all resolved as little shields.

-Noel