Focus Stacking Studio

User Manual

Overview

MJKZZ Focus Stacking Studio is a comprehensive solution designed to

control rail systems for focus stacking. These include single axis focus
stacking rail systems as well as multi-axes rail systems for Stack-n-Stitch
operations. Flexible design allows different configurations and
combinations of different rails and controllers. Key features include the
following:

⦁ Single rail systems

⦁ Multi-axes rail systems for Stack-n-Stitch

⦁ Graphical magnification measurement

⦁ Step size calculator

⦁ Visualization of Stack-n-Stitch operation

⦁ Allows flexible configurations of rail and controller

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 Here is an example of Focus Stacking Studio in use

Basic Concepts
Before proceeding with how to use Focus Stacking Studio, there are some
basic concepts that are used throughout this document (as well as focus
stacking in general).

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Most focus stacking rail system consists of a moving block, driven by
either lead screw or belt or other mechanism. Step motor is involved, too,
to automate the process. So, here are some basic concepts regarding step
motor and controller and they apply to all axis:

⦁ Pitch - this refers how far the moving block travels when motor
rotates a full revolution. For lead screw system, this is often referred
to as lead screw pitch. For belt driven system, this is the
circumference of wheel driving the belt. For rotational axis, this
value is always 360

⦁ Turn/Revolution - this is the number of native steps per revolution

for the motor. Typical values are 200 and 400 (1.8 degrees or 0.9
degrees) for step motors. Note, native step means a full step without
micro stepping.

⦁ Micro Step - Most modern step motor controller can sub-divide a

fulll step of a step motor into finer steps, this is called micro
stepping. This allows finer movement of a step motor

⦁ Power - MJKZZ step motor controllers have the capability of

supplying different levels of current to step motors being driven. In
Focus Stacking Studio, the current level to move step motor is
considered as Power.

⦁ Idle Power - When step motor is not moving, it still draws current
and this current can cause motor to heat up. Therefore, it is a good
idea to supply lower current if the motor is not moving. This is called
Idle Power

⦁ Reverse - depends on how a rails is installed, very often the motor

moves in a direction that is contrary to our intuition. To correct this,
some step motor controller allows reverse of direction.

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 An Example of Parameters For Step Motor

Beside information about step motor and controller, it is also necessary to

know information about camera and optical system, such as dimention of
camera sensor and magnification, DoF of optics.

⦁ Sensor Width - this refers to the width of camera sensor, in

millimeters. It is used to determine the step size along X axis (or the
axis parallel to "the width".

⦁ Sensor Height - this refers to the height of camera sensor, in

millimeters. It is used to determin the step size along Y axis (or the
axis parallel to "the height"

⦁ Magnification - this refers to true physical magnification of optics.

Note this is not the effective magnification, rather the true optical
magnification. There is a utility tool in Focus Stacking Studio to
determine this

⦁ DoF - this refers to depth of field of the optics used. This is an

important factor to determine step size for the stacking axis
(normally the Z axis)

⦁ Min Overlap - this refers to minimum desired overlap for Stack-n-

Stitch operation. It is the minimum because the actual overlap could
be larger than this value

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 An Example Of Camera Parameters

Timing is also critical for a successful stacking session. Here are some of
them that Focus Stacking Studio requires

⦁ Wait - this is the amount of time system should wait before taking a
picture AFTER moving. This is needed because the rail system needs
some time to settle down and stablize

⦁ Hold - this is the amount of time system should wait before moving
again AFTER taking a picture. This is necessary because for some
operation, exposure time can be very long, if the rail moves during
exposure, images will be blurry

⦁ Snap - this is the amount of time the system should keep the signal
to take a picture active because it might take camera some time to
expose an image

Basic Operations
Here are some of the basic operations, connecting to controller, moving
rails, etc
USB Connection
Focus Stacking Studio supports multiple rails designed by MJKZZ. There
are two basic connection methods, namely, USB and WiFi. USB connection
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is essentially a USB-to-Serial port. Focus Stacking Studio can
automatically detect what a connected rails system is, ie, a single axis one
or a multi-axes one.

Connecting To An USB Based Rail

To connect to a rails system via USB, simply select menu

File->Connect->USB
After that, a USB connection dialog will pop up with a list of available COM
ports, like below

It is important to select the right COM port -- pick the one that is actually

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connected to the rail system of interest.
WiFi Connection
For those MJKZZ focus stacking controller with WiFi capability,
connection can be made via WiFi. Connecting to a WiFi capable device is
as simple as pulling down the File->Connect menu and select WiFi, as
shown below

Access To WiFi Connection

WiFi Configuration
By factory default, it is most likely that the WiFi SSID and password will
not work in your working environment. Therefore, it is necessary to set
SSID and password for WiFi.

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 Scren Shot Of WiFi Setup

Here are steps to do so:

⦁ Connect the controller via USB

⦁ If the device is WiFi capable, Focus Stacking Studio will be able to

configure it for WiFi setup -- the menu Tools->WiFi Setup will be
enabled

⦁ SSID - this is the SSID of WiFi network the device should connect to.

⦁ Password - this is the password needed to join the WiFi netowork

⦁ Turn On WiFi - check this if you want to turn on WiFi feature and the
device will automatically to the WiFi network next time it is
powered on.
Trouble Shooting WiFi Connection
Windows firewall security might block some WiFi connection, so it is
possible to encounter the following:

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 Windows Defender Firewall Warning Screen

Clicking on Allow Access button to enable Focus Stacking Studio to

communicate with WiFi enabled stacking controller. Once Focus Stacking
Studio is allowed to access features on network, it needs to be shut
down and restarted.
If Focus Stacking Studio is accidentally blocked from access network
features, here are steps to re-enable it.
Step 1 - click on Windows Startup icon at the lower left corner of
Windows and type 'Firewall', then select 'Windows Defender Firewall with
Advanced Security'

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Step 2 - starting up 'Windows Defender Firewall with Advanced Security',
click on 'Inbound Rules' and here is a screen shot

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If 'fss' is being blocked, delete all rules associated with it. Then restart
Focus Stacking Studio, allow access and then restart it again.
Camera Parameters
As discussed in basic concept setion, information of camera is required.
Normally by default, these information are hidden. These information can
be made to be visible by selecting View->Show Setup, like below.

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Once Show Setup is selected, data for step motor and controller will be
visible and can be editted.

Timing Parameters
To set or modify timing information as described in basic concept section,

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simply choose to show timing setup under menu View like below.

Axis Position And Status

Here is an example of screen showing Stack-n-Stitch setup.

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⦁ Current Position - this is the current position of an axis
⦁ Specimen Start - this is start position along an axis. It can be set to
current position value by clicking on the 'Set' button
⦁ Specimen End - this is the end position along an axis. It can be set to
current position value by clicking on the 'Set' button

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 ⦁ Step Size - this is the actual step size for the specific axis
⦁ Actual Overlap - once start, end positions, and minimum overlap are
specified, this is the actual overlap for that axis. It should be equal to
or greater than the minimum overlap specified in General section
⦁ Count - this is the number of steps for the specific axis. Note it is a
calculated value, not changable for X, Y, or Z axis. It is editable for R
axis
⦁ Rotation - in case of rotation axis, this is the amount to rotate, sort of
like step size for linear axes (like X or Y axis)
⦁ Y Index - for Z axis, it is necessary to specify which cell the Z is for.
The Y index specifies the cell index along Y axis. It can be changed by
clicking on '<' or '>' button
⦁ X Index - for Z axis, it is necessary to specify which cell the Z is for.
The X index specifies the cell index along X axis. It can be changed by
clicking on '<' or '>' button
⦁ Rotation (Index) - this is the index for R axis.

Moving Along Axes

⦁ Moving along X axis -- use Left or Right arrow keys
⦁ Moving along Y axis – use Up or Down arrow keys
⦁ Moving along Z axis – use PageUp or PageDown keys

Game Controller Support

There are other ways to move and navigate tiles, one such support is XBox
game controller. It makes it much easier to move the rails around.

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⦁ Marker 1 - use this joystick to move rails in X and/or Y direction
⦁ Marker 2 - use these digital pad buttons to move current cell selection
⦁ Left and Right Analog Triggers - use these trigger button to move along
Z axis
⦁ Left and Right Shoulder Triggers

⦁ If A button is pressed and Left Shoulder Trigger is pressed at same

time, the Start Position of R axis will be set to the current R position
⦁ If A button is pressed and Right Shoulder Trigger is pressed at same
time, the End Position of R axis will be set to the current R position
⦁ If X button is pressed and Left Shoulder Trigger is pressed at same
time, the Start Position of X axis will be set to the current X position
⦁ If X button is pressed and Right Shoulder Trigger is pressed at same
time, the End Position of X axis will be set to the current X position
⦁ If Y button is pressed and Left Shoulder Trigger is pressed at same
time, the Start Position of Y axis will be set to the current Y position
⦁ If Y button is pressed and Right Shoulder Trigger is pressed at same
time, the Start Position of Y axis will be set to the current Y position
⦁ If None of the X, Y, A buttons are pressed, Left Should Trigger will
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 set Start Position of Z axis to current Z position
⦁ If None of the X, Y, A buttons are pressed, Right Should Trigger will
set End Position of Z axis to current Z position
⦁ Button B - use this button on the controller to lock or unlock game
controller input. This is useful to prevent accidental change.

Saving and Loading Parameters

There are lot of data and parameters involved for stacking and these data can
be saved or loaded back. All of these can be done via the File menu

⦁ Open - loads back previously saved data

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 ⦁ Save - save current settings
⦁ Save As - save current settings into another file. This is useful, for
example, one might have one setting for one set of optics and another for
others.

Detecting Attached Devices

Many MJKZZ stacking controllers can be combined together to support
more axes. For example, after connectiong to X, Y, and Z axis controllers,
when R axis is attached to the system, it can be added via 'Scan Devices'
under Tools menu

Views

Basically, Focus Stacking Studio have two views at any time. One is
information view, always resides on the left side. It is structured as
collapsible lists. The right hand side usually is occupied by various views
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specific to selected function, such as tile view, magnification determination
view, XY table alignment view, etc. These functional views always take up
the right hand side of screen.

Tile View

This is the view that shows current interaction of tiles. For example,
moving cursor over this view will highlight a particular tile. Here are list
of features:

⦁ Hovering over a tile using a mouse will highlight its border. Here are
the meaning of border colors
⦁ Red – when a particular tile does not have its Z axis setup, there
will be a red dot shown at upper right corner of its bounding box.
When mouse hovers over it, the border will be highlighted with
red.
⦁ Blue – this is the color for current tile selection.
⦁ Green – if a tile has its Z axis setup, there will be a green dot
shown at upper right corner of its boundary. When mouse hovers
over this tile, its border will be highlighted as green
⦁ Single Click on a tile will make that tile as current tile selection.
However, physical rail is not moved to that physical position. To
move it physically, press HOME or as following, double click on the
tile.
⦁ Double Click on a tile will make that tile as current tile selection, as
well as physically moving the rail to its physical position. If tethered
camera operation or "just watch foler" is set, an image will also be
captured for that tile. More on this later

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Another way to select current tile is to use mouse, just a single click on the
right hand view where tiles are shown. However, selecting current tile
this way do not actually move the rail to that position. To move the
physical rail to the physical position of current selected tile, double click on
the selected tile.

Magnification Measurement View

It is important to know actual magnification of optical system, inaccurate
magnification value could lead to many mis-calculation and displays. For
example, significantly wrong magnification value can leas to images being
tiled incorrectly -- to much overlap or gaps between tiled images
Access magnificantion measurement view as following:
Tools->Magnification

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Magnification Menu

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 An Example Of Magnification Calculation

There are several steps to accurately measure magnification. Here they

are:

⦁ Make sure camera sensor dimension data are accurate

⦁ Take a picture of a ruler and load that image into Magnification View

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 ⦁ Enter the physical length for two segments of the image at the
bottom of the view

⦁ While in magnification view, hold down SHIFT key, now cursor will
turn into a cross. Draw a line from one end of the intended segment
to another part, while drawing, magnification will by displayed
dynamically

⦁ The calculated magnification value can be copied to the general

section by clicking on 'Copy'

XY Alignment View
It is also very important that the X and Y axis are perpendicular to each
other because all calculations are based on such assumption.

Tethered View

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 Access To Tethered

Camera tethering is well known and well received among photographers.

Focus Stacking Studio can benefit from tethered operation because
images can be pulled into computer by camera's tethering application.
Here is a screen shot of Tethered dialog.

⦁ Tethering Application - by default there are four supported tethering

applications, they are Capture One, Lightroom, EOS Utility, and Sony
Remote These are the application that Focus Stacking Studio can
send a command to take a picture. This is convenient in many
situations

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 ⦁ Watch Folder - this is the folder where a tethering application saves
images to. Even if Tethering Application is not one of listed above, it
still works as long as the folder images are saved to is known.

⦁ Start Tethering - this button starts both tethering operation and

watching the "Watch Folder" as images come in. The tethering
operation means that images are taken by sending a command to the
specified tethering application instead of letting stacking controller.
This is very helpful for those cameras that do not have a remote
shutter port, but is supported by one of the tethering application

⦁ Just Watch Tethered - this button enables 'watch' operation. This

means that Focus Stacking Studio does not rely upon tehtering
application to take a picture, it relies up the stacking controller. But
it will be monitoring the folder images are pulled in, therefore being
able to display them as they come in

⦁ Stop Tethering - this stops both tethering (if enabled) and watch

Some more comments worthy more emphasizing about Tethered View

⦁ It is NOT necessary to specify a 'Tethering Application' if there is no

need to trigger camera via the tethering application.

⦁ Watch Folder is where a tethering application save images pulled

from camera. It does not matter how images are pulled, only where
images are pulled to and saved

⦁ Preview of stitched image relies upon 'Watch Folder' because it

needs those images to preview

Stacking View

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If a single axis stacking controller is connected, it is better to use this
view, to make it less complicated. However, if a multi-axes controller is
connected but you only want to do single axis stacking, this is also good
view as it simplifies operation

Notice above picture, a three axes controller is connected, but the

stacking view is shown. Notice at the bottom, R, X, and Y axes are set to 1,
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1, and 1.

Game Controller X Support

Focus Stacking Studio supports XBox game controller and it will
automatically detect if driver for XBox game controller is installed or not.
If XBox game controller is available but you do not wish to use for
whatever reasons (such as accidental motion), it can be disabled by
uncheck (toggle) the menu item

Calculator
Focus Stacking Studio features a step size calculator for variety of optical
combinations. This is especially important for beginners, as well as some
experienced stackers. The calculation is on the conservative side, ie, the
calculated value tends to be smaller than what might be needed. This is to
ensure the calculated value 'works'. This is true particularly for high
magnifications where end result is high sensitive to parameters entered, a
slight deviation will cause big difference in result.
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Generic Lens
This is for optical system using generic lenses by extending it using
extension tubes.
⦁ f-stop - this is the f-stop the lens is set to, the smaller aperture
(larger f-stop number), the larger step size
⦁ Magnification - this is the actual/measured magnification either
using the Magnification tool in Focus Stacking Studio or some other
means.
⦁ Effective f-stop - this is a calculated value. As result of extension and
modification of a generic lens, the aperture seen by the camera
sensor tend to be different from actual physical one
⦁ Step Size - this is a calculated value based on input parameters

Microscope Objective
This is for those optical system employing microscope objectives.
⦁ NA - this is the NA value of an objective, part of key specification of
an objective
⦁ Objective Magnification - this is the specified magnification of an
objective
⦁ Sensor Type - this is the sensor type of camera

Lens with Close-Up Filter

This is for those optical systems using a dioptor filter in front of a lens for
higher magnification
⦁ Dioptor Value - usually this is specified by the dioptor manufacturer

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 ⦁ Primary Lens Focal Length - this is the focal length of the main lens
the dioptor filter is attached to. If a zoom lens is used, enter the real
focal length, by reading it off the zoom lens
⦁ Primary Lens Magnification - this is the magnification value when
the dioptor is not attached.
⦁ Extension Tube Length - if any extension is used, this is its length. If
no extension tube is used, enter zero

Lens With Extension

This is for those optical systems using extension tubes on a lens.
⦁ Primary Lens Focal Length - this is the focal length of the lens used
⦁ Primary Lens Magnification - this is the magnification without
extension tube
⦁ Extension Tube Length - this is the total length of extension

Stacked Lenses
A macro lens can be created by stacking two lenses together. When
stacking two lenses, set the aperture of the primery lens to its maximum
and use the aperture of reversed lens to control lights
⦁ Primary Lens Focal Length - the focal length of primary lens which is
the one attached to the camera.
⦁ Reverse Lens Focal Length - the focal length of the lens that is
mounted on the primary lens in reverse.
⦁ Extension Tube Length - the length of extension tube if any, enter
zero if none

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 ⦁ f-stop - this is the f-stop of the reversed lens.

Reverse Lens
It is a common practice to reverse a normal lens as a macro lens.

⦁ Reverse Lens Focal Length - the focal length of reversed lens

⦁ Reverse Lens Magnification - magnification of the reversed lens in

normal orientation

⦁ Extension Tube Length - this is the length of extension if any. Enter

zero if no extension tube used

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