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Author Topic: Stackshot and Helicon remote  (Read 2803 times)
Jim Kasson
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« on: November 25, 2013, 05:55:50 PM »
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I'm going to be making some focus-stacked macros. I will be using Helicon Focus for image processing. I've bought the Stackshot rail, and have figured out how to use it with its own controller. Since it was cheap to buy when I was buying Focus, I bought the Android version of Helicon Remote. I have it running on a Nexus 7.

My first problem is how to hook up the rail and the camera, a D800E, to the Nexus 7. I have a OTG USB cable, so I can hook up one USB device to the Nexus 7. I tried hooking up just the rail, but Helicom remote doesn't recognize it. The Helicon Remote help file says to hook both the camera and the rail up to the computer running Helicon Remote.

There's a diagram that says the same thing on the Cognisys web site.

Does that mean I need a USB hub? I set one up, and hooked the Nexus 7 up to the uplink side, and the camera and the rail to the downlink side.

Helicon remote recognized the camera, but gives no indication that it recognizes the rail. Actually, I don't have any idea what such an indication would look like -- there seems to be no place in the software where the rail should be. I have a Zeiss 100mm f/2 ZF lens on the camera. when I try to focus with Helicon Remote, nothing happens. I figure that it should move the rail when I hit the focus arrows.

I guess I'm doing something wrong. Anybody have an idea what?

Is this game worth the candle? Finding a battery powered USB hub, having a rat's nest of cables, etc sound messy in the field. Does Helicon remote bring enought to the party to make it worthwhile for me to continue the struggle to get the camera, the rail, the Nexus 7, and the software all playing together?

Thanks for any help.

Jim
« Last Edit: November 25, 2013, 07:07:13 PM by Jim Kasson » Logged

Dustbak
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« Reply #1 on: November 26, 2013, 02:48:01 AM »
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I use the same setup (stackshot plus helicon remote) however I use it with a HB and have not used it with the D800.

I think there are several things at play. The software should be able to see and steer the rails, I prefer using the control box on the stackshot. Eg. Focus, set the number of shots, beginpoint and endpoint, off you go....

Focus from within Helicon probably does what it says, focus your camera. Since you are using a MF lens I guess that is not an option. Try using an AF lens just to see what happens, I think that will focus the lens.

I found there are a number of options on how to use combinations of equipment, some have quirks, nothing is perfect (yet) so you have to find something that works for you. Preferably reliable Wink
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Jim Kasson
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« Reply #2 on: November 26, 2013, 04:13:41 PM »
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Thanks for getting back to me on this. It's nice to be able to talk to someone with a similar setup.

...The software should be able to see and steer the rails...

How do you know if Helicon remote can see the rails? If by steer, assuming you mean move the carriage back and forth on the rails, how do you get it to do that?

I prefer using the control box on the stackshot. Eg. Focus, set the number of shots, beginpoint and endpoint, off you go...

If you're using the Stackshot control box to set the number of shots, begin and end points, what does Helicon Remote do?

Focus from within Helicon probably does what it says, focus your camera. Since you are using a MF lens I guess that is not an option. Try using an AF lens just to see what happens, I think that will focus the lens.

I think it would focus the lens if I had an AF lens set to AF; it does that with no rail attached. But that's not what I want. I want the lens to stay focused to the same distance for all the shots in the stack, and the rail's position to control what's in focus.

Thanks again.

Jim
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bjanes
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« Reply #3 on: November 26, 2013, 09:56:03 PM »
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I think it would focus the lens if I had an AF lens set to AF; it does that with no rail attached. But that's not what I want. I want the lens to stay focused to the same distance for all the shots in the stack, and the rail's position to control what's in focus.

With the manual focus lens, one has no choice but to focus by use of a focusing rail. With an auto focus lens, one can use the focusing rail, moving the camera to successive focus points, or leave the camera stationary and focus by adjusting the lens. The results are somewhat different and I did a simple experiment with the MicroNikkor 60mm f/2.8 AFS on the D800. I arranged some rulers spaced 5 cm apart, with the first ruler about 40 cm from the focal plane of the sensor and created stacks using both methods. With the focusing rail, the distance from the camera to each element (ruler) in the stack is 40 cm. Using the lens to focus on the elements, the distance to each element of the stack varies.

Here is a composite of the results of both methods showing the first and last ruler in the stacks and the results with Helicon Focus using default parameters:


Here are the results of the focus stacks at larger magnification

Stack with focusing by the lens:


Stack with focusing via the rail. Note the artifact on the closest ruler, which was not present on the individual shot of that ruler:


For further illustration, here are shots of the closest ruler in both series. They should be the same, but the magnification is slightly different due to camera placement.

Focus rail stack, first image:


Lens adjustment stack, first image:


Finally, this table shows the magnification of each image in the stacks. With the focusing rail, the magnification is reasonably constant since the object distance of each shot of the series is the same, but when focusing with the lens the distance to each ruler in the series varies. The image height of the sensor is 4912 pixels and 2.4 cm. The image size of 5 cm on the ruler was determined by measuring the number of pixels occupied by 5 cm on the ruler and calculating the percentage of the picture height taken by this 5 cm and multiplying by 2.4 cm to obtain the image height of the 5 cm segment. The magnification is that height divided by 5.0



Personally, I prefer the results obtained by focusing the lens rather than using the rail.

Bill

 
« Last Edit: November 26, 2013, 10:27:31 PM by bjanes » Logged
Dustbak
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« Reply #4 on: November 27, 2013, 02:22:12 AM »
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Thanks for getting back to me on this. It's nice to be able to talk to someone with a similar setup.

How do you know if Helicon remote can see the rails? If by steer, assuming you mean move the carriage back and forth on the rails, how do you get it to do that?

If you're using the Stackshot control box to set the number of shots, begin and end points, what does Helicon Remote do?

I think it would focus the lens if I had an AF lens set to AF; it does that with no rail attached. But that's not what I want. I want the lens to stay focused to the same distance for all the shots in the stack, and the rail's position to control what's in focus.

Thanks again.

Jim

Helicon focus should be able to move the rails back and forth and take a predetermined number of shots. Helicon Focus is supposed to be able to this automated with a number of bodies (including some Nikons).

This is what I use the control box for. Since I use the rails primarily with the Hasselblad, Helicon Focus is not automated for the HB.

In my setup the control box takes the images, these end up in Hasselblad phocus software, get converted to Tiff and I use Helicon Focus to create the end result.

In my setup the rails determines what is in focus and what not. My way of working with it is not completely automated, I need to set the number of shots, begin and endpoint. After that I need to import the files into Helicon Focus. Not completely automated but still pretty fast if you get the hang of it.
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BartvanderWolf
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« Reply #5 on: November 27, 2013, 04:10:41 AM »
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Personally, I prefer the results obtained by focusing the lens rather than using the rail.

Hi Bill,

That's understandable, given that natural perspective at this shooting distance is probably preserved better by (internal) focusing (smaller change in entrance pupil position). At larger magnification factors, e.g. small jewelry or watch-face detail, a focus-rail setup is often better (because of the much narrower DOF at such magnification factors). Subject matter also makes a big difference, especially occlusions can cause issues (using the correct stacking method also makes a difference, and one can also combine (with) the results from different methods).

Rik Littlefield, the author of the Zerene software, has a nice article dedicated to that ring-versus-rail trade-off, here.
He basically concludes that in general, subjects at the size of a raisin are at the tipping point between both techniques. Of course, as I've mentioned before, it also depends on the subject matter, and of course one can only use a rail with manual focus lenses (assuming automated sequence capture).

Cheers,
Bart
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bjanes
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« Reply #6 on: November 27, 2013, 07:46:48 AM »
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Hi Bill,

That's understandable, given that natural perspective at this shooting distance is probably preserved better by (internal) focusing (smaller change in entrance pupil position). At larger magnification factors, e.g. small jewelry or watch-face detail, a focus-rail setup is often better (because of the much narrower DOF at such magnification factors). Subject matter also makes a big difference, especially occlusions can cause issues (using the correct stacking method also makes a difference, and one can also combine (with) the results from different methods).

Rik Littlefield, the author of the Zerene software, has a nice article dedicated to that ring-versus-rail trade-off, here.
He basically concludes that in general, subjects at the size of a raisin are at the tipping point between both techniques. Of course, as I've mentioned before, it also depends on the subject matter, and of course one can only use a rail with manual focus lenses (assuming automated sequence capture).

Bart,

Thanks for the link to an excellent article. It is good to know the pros and cons of each method in a given situation.

I would think that when using focusing by rail the differences in perspective could be mitigated by using a lens with a longer focal length.

You mention internal focusing, which raises an interesting question. The lens that I used uses internal focusing. When focusing at closer distances, the lens is not extended but rather the internal elements of the lens are re-arranged and the effective focal length of the lens shortens (focus breathing). In a focus stack, the picture elements closer to the camera are imaged at a shorter focal length, decreasing image magnification. The more distant elements are taken with a longer focal length, increasing the magnification of those elements and thus mitigating the differences in magnification between near and far picture elements, similar to the situation with the focus by rail. Is this a disadvantage?

Regards,

Bill
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Jim Kasson
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« Reply #7 on: November 27, 2013, 10:15:35 AM »
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Thanks very much. Bill and Bart, for your insights on AF vs rail, and the effect of modern internal focusing lenses --which have, effectively, a combination focus/zoom ring -- on stacked image perspective. Bill, your examples are great.

I remember some time in the early 90s when I got the idea of doing what's now called focus stacking. I put a Nikon 120mm macro lens on a 4x5 Arca-Swiss monorail camera, and made three exposures focusing by moving the front standard. I noticed that the magnification changed. Then I made three exposures focusing by moving the back standard. Different perspective. Then I moved both the same amount, effectively doing what the rail does, and I had a third set of perspectives. I scanned all nine negs with an Optronic ColorGetter (that's how long ago it was), and tried to write some software to merge the images. It became clear early on that I'd need to take the perspective into account. That turned a problem that I could wrap my head around into one that was going to take a lot of work, and I dropped the project. I was supposed to be working on device-independent color, so this was definitely a diversion. IBM had a journal that they used to publish ideas that they didn't want to patent, but didn't want anybody else to be able to patent. I wrote up a submission, and forgot about it. I don't know if it was ever published.

What goes around, comes around, and now people have apparently solved the geometry problem on which I broke my pick. And I'm a customer.

I think I'm going to start with the rail, since the two lenses I want to use the most on this project, the Zeiss 100mm and the Coastal Optics 60mm, are both manual focusing lenses. I'll play with the Nikon 60mm and 105mm if I want to try some focus-mediated stacking. It would seem that each internal-focus lens will have its own geometry/perspective, depending on the way the designer traded off moving the lens and changing its focal length as it is "focused".

Again, thanks for all your help.

Jim
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Jim Kasson
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« Reply #8 on: November 27, 2013, 10:22:00 AM »
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Helicon focus should be able to move the rails back and forth and take a predetermined number of shots. Helicon Focus is supposed to be able to this automated with a number of bodies (including some Nikons).

You mean Helicon Remote?

This is what I use the control box for. Since I use the rails primarily with the Hasselblad, Helicon Focus is not automated for the HB.

In my setup the control box takes the images, these end up in Hasselblad phocus software, get converted to Tiff and I use Helicon Focus to create the end result.

In my setup the rails determines what is in focus and what not. My way of working with it is not completely automated, I need to set the number of shots, begin and endpoint. After that I need to import the files into Helicon Focus. Not completely automated but still pretty fast if you get the hang of it.

It sounds like you're not using Helicon Remote. I think, for the images I make with the rail, that I won't use it either. Even if can get it working, I don't see how it's going to help much. The only advantage I see is automatic calculation of the number and location of the images, and I can do that like it seems you are, with a DOF table. The other thing Helicon Remote could do for me is provide me with a larger live view window, but I realy don't see any reason to use live view in this project at all.

We'll see what happens when I get into the field.

Thanks for you help.

Jim
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bjanes
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« Reply #9 on: November 27, 2013, 10:47:15 AM »
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Thanks very much. Bill and Bart, for your insights on AF vs rail, and the effect of modern internal focusing lenses --which have, effectively, a combination focus/zoom ring -- on stacked image perspective. Bill, your examples are great.

I remember some time in the early 90s when I got the idea of doing what's now called focus stacking. I put a Nikon 120mm macro lens on a 4x5 Arca-Swiss monorail camera, and made three exposures focusing by moving the front standard. I noticed that the magnification changed. Then I made three exposures focusing by moving the back standard. Different perspective. Then I moved both the same amount, effectively doing what the rail does, and I had a third set of perspectives. I scanned all nine negs with an Optronic ColorGetter (that's how long ago it was), and tried to write some software to merge the images. It became clear early on that I'd need to take the perspective into account. That turned a problem that I could wrap my head around into one that was going to take a lot of work, and I dropped the project. I was supposed to be working on device-independent color, so this was definitely a diversion. IBM had a journal that they used to publish ideas that they didn't want to patent, but didn't want anybody else to be able to patent. I wrote up a submission, and forgot about it. I don't know if it was ever published.

What goes around, comes around, and now people have apparently solved the geometry problem on which I broke my pick. And I'm a customer.

I think I'm going to start with the rail, since the two lenses I want to use the most on this project, the Zeiss 100mm and the Coastal Optics 60mm, are both manual focusing lenses. I'll play with the Nikon 60mm and 105mm if I want to try some focus-mediated stacking. It would seem that each internal-focus lens will have its own geometry/perspective, depending on the way the designer traded off moving the lens and changing its focal length as it is "focused".


Jim,

I am impressed by the quality of the lenses available to you: Zeiss 100 macro, Zeiss 135 mm Apo, and the Coastal Optics 60 mm. Together with your technical expertise you are in an excellent position to publish high quality reviews and I hope you will share your findings.

Using a longer focal length lens could mitigate perspective problems. The 150 mm Sigma macro appears attractive, but they have had quality control problems in the past and purchasing the lens would be somewhat risky unless you can do extensive testing to verify that you have a good sample. Personally, I would be more interested in the Nikkor 200 mm macro if they would update it with the modern lens coatings and AFS focusing rather than the old screw drive mechanism. It is due for an update.

I have seen good macro results from the Nikkor 300 mm f/4 AFS, but it loses automation if an extension ring is needed. I have the Canon 77 mm 500D diopter which could be used on both my Nikkor 300 f/4 and my Zeiss 135 mm APO, but in the latter case it would be a shame to degrade such a fine optic by introducing another element in the optical path. What do you think of these possibilities?

Regards,

Bill
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BartvanderWolf
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« Reply #10 on: November 27, 2013, 11:27:47 AM »
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Bart,

Thanks for the link to an excellent article. It is good to know the pros and cons of each method in a given situation.

Hi Bill,

Yes, Rik is very knowledgeable in Photomacrography/micrography. He made a good summary of the various scenarios.

Quote
I would think that when using focusing by rail the differences in perspective could be mitigated by using a lens with a longer focal length.

You mention internal focusing, which raises an interesting question. The lens that I used uses internal focusing. When focusing at closer distances, the lens is not extended but rather the internal elements of the lens are re-arranged and the effective focal length of the lens shortens (focus breathing). In a focus stack, the picture elements closer to the camera are imaged at a shorter focal length, decreasing image magnification. The more distant elements are taken with a longer focal length, increasing the magnification of those elements and thus mitigating the differences in magnification between near and far picture elements, similar to the situation with the focus by rail. Is this a disadvantage?

It's hard to predict accurately, but it ultimately depends on whatever produces the smaller shift of the entrance pupil position. We have no general idea of how much that moves around with an internal focusing lens, they are all different, so it can only be determined for a specific setup.

There will also be magnification differences between the individual tiles of a stack, either caused by variable focal length or extension/distance (with the rare exception of focusing with truly tele-centric lenses). Therefore images will almost always need to be resampled to allow accurate registration and flattening to a single result file. Dedicated focus-stacking applications allow to use much better algorithms than e.g. Photoshop to maintain as much of the capture detail despite the resampling.

So, in the end it all depends a lot on the specifics, manual focus, optical design, distance or magnification factor, required acquisition speed, repeatability, etc., etc. No simple solutions, but the software is very accommodating to handle various scenarios.

It can also help to play out some scenarios with my DOF output quality planning tool, which offers a section (3.) to estimate the focus stacking requirements. Of course it can only be a rough guide when focal lengths and magnification factors/distances change in all directions, but then it would already be close to impossible to nail the focus distance exactly if we do not know where the front principal plane of the lens is exactly situated.

Cheers,
Bart

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Peter McLennan
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« Reply #11 on: November 27, 2013, 11:55:09 AM »
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An interesting discussion.  As a relative newcomer to focus stacking, I've run up against the limitations of PSCS6 "auto align layers" and "auto blend "layers".  Do specialized software tools like Zerene Stacker and Helicon Focus offer significant advantages over my all-Photoshop workflow?
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Jim Kasson
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« Reply #12 on: November 27, 2013, 12:07:47 PM »
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Using a longer focal length lens could mitigate perspective problems. The 150 mm Sigma macro appears attractive, but they have had quality control problems in the past and purchasing the lens would be somewhat risky unless you can do extensive testing to verify that you have a good sample. Personally, I would be more interested in the Nikkor 200 mm macro if they would update it with the modern lens coatings and AFS focusing rather than the old screw drive mechanism. It is due for an update.

I have seen good macro results from the Nikkor 300 mm f/4 AFS, but it loses automation if an extension ring is needed. I have the Canon 77 mm 500D diopter which could be used on both my Nikkor 300 f/4 and my Zeiss 135 mm APO, but in the latter case it would be a shame to degrade such a fine optic by introducing another element in the optical path. What do you think of these possibilities?

Bill,

I started the project with the Sigma 180mm macro, and got results that were compromised both by diffraction (too small an f-stop) and vibration. That's what lead me to stacking in the first place.

My testing has lead me to the opinion that, if I can avoid it, I shouldn't use lenses that are heavy enough to require focusing collars, like the Sigma 180 and some of the lenses you mention. Here's an admittedly extreme example of mirror-slap decay with the Nikon f/2.8 400mm lens on the D800E. You may want to look here and some of the preceding posts to get the methodology, but basically, I'm photographing an oscilloscope trace at a distance to get a plot of the sensor-level effect of camera vibration.

I'm pre-triggering the mirror on all the pictures I'm doing now, but even so, the vibrations when you attach the tripod to the lens collar are greater than situations where you can attach the the tripod to the camera body, even taking into account the fact that the longer-focal-length lenses produce greater blur on the sensor for the same motion. I haven't wrung all that out with testing, but I've formed an opinion.

In addition, there are places where I'm having trouble backing up far enough with the 180mm.

So I think I'll try the 100 and the 60 and see what happens with the perspective. If it's a problem, I'll take your advice and explore longer focal lengths. I have the old Nikon 200mm macro that you mentioned, which I haven't used since I stopped scuba diving with it.

Jim
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Jim Kasson
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« Reply #13 on: November 27, 2013, 12:58:13 PM »
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It can also help to play out some scenarios with my DOF output quality planning tool, which offers a section (3.) to estimate the focus stacking requirements. Of course it can only be a rough guide when focal lengths and magnification factors/distances change in all directions, but then it would already be close to impossible to nail the focus distance exactly if we do not know where the front principal plane of the lens is exactly situated.

This is great, Bart! I've bookmarked it in my cellphone. Have you considered doing a version with less explanatory text for small screen users?

Thanks,

Jim
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BartvanderWolf
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« Reply #14 on: November 27, 2013, 01:33:33 PM »
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An interesting discussion.  As a relative newcomer to focus stacking, I've run up against the limitations of PSCS6 "auto align layers" and "auto blend "layers".  Do specialized software tools like Zerene Stacker and Helicon Focus offer significant advantages over my all-Photoshop workflow?

Hi Peter,

The benefit of Photoshop is that it is relatively simple to do focus-stacking, when it works as intended. However, there are very few things one can do to solve imperfections, besides tedious retouching. Also, the resulting resolution can be a bit lower than with the dedicated applications, due to the less advanced resampling algorithms.

Because Zerene Stacker and Helicon Focus offer many more options and control, they also have a longer learning curve, but the results are often superior (when used with optimal settings). As usual, a special technique like focus-stacking also comes with certain rules and limitations, so learning the ropes can also take a bit of experimentation. Of course, the reward is that it beats physics and allows to achieve otherwise impossible results.

One of the more advanced possibilities is to also produce a 'depth-map' from the stack, which allows to adjust DOF afterwards based on an image with huge DOF combined with a filter that blurs based on depth information.

Cheers.
Bart
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ACH DIGITAL
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« Reply #15 on: November 27, 2013, 01:48:50 PM »
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Hi guys, I've been using Helicon Focus for macro photography for a long time. I use a D800 and several macro lenses. The result 98% of the time are fantastic. Few times, when shapes are complicated with lost of fiber and stuff is that I get some halos.
I've never needed a focusing rail for this.

ACH
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Antonio Chagin
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« Reply #16 on: November 27, 2013, 01:51:46 PM »
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This is great, Bart! I've bookmarked it in my cellphone. Have you considered doing a version with less explanatory text for small screen users?

Hi Jim,

Considered, yes, but no final plans yet on how to do it. In this thread a few others have expressed interest, so am considering it if resources allow it.

I did try to condense most input fields in small areas, to allow hitting the input boxes a bit easier on mobile devices when zoomed-in, but there is still a lot that would need adjustment (info icons instead of tooltips, multiple tabs or pages, etc.). Once loaded, the application can be left on its own browser tab, it does not need to 'phone home' or place cookies, so no connection required until one refreshes the entire page.

Cheers,
Bart
« Last Edit: November 28, 2013, 04:04:03 AM by BartvanderWolf » Logged
BartvanderWolf
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« Reply #17 on: November 27, 2013, 01:57:41 PM »
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Hi guys, I've been using Helicon Focus for macro photography for a long time. I use a D800 and several macro lenses. The result 98% of the time are fantastic. Few times, when shapes are complicated with lost of fiber and stuff is that I get some halos.
I've never needed a focusing rail for this.

Hi Antonio,

A lot can be done without an automatic focus rail. But it is a real time saver on larger stacks, e.g. 100+ slices. Of course one also doesn't have to focus by eye with manual focus lenses.

Cheers,
Bart
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« Reply #18 on: November 27, 2013, 03:53:29 PM »
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Hi Antonio,

A lot can be done without an automatic focus rail. But it is a real time saver on larger stacks, e.g. 100+ slices. Of course one also doesn't have to focus by eye with manual focus lenses.

Cheers,
Bart

Thanks Bart.
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Antonio Chagin
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Peter McLennan
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« Reply #19 on: November 27, 2013, 06:29:48 PM »
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Thanks Bart. Time to upgrade my procedure.
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