image viewer

ver. 1.8

White Rabbit Corporation1

Index

1. Introduction

What is Molcer? What can it do for you?

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2. Basic Operation

Open file4

Overwrite molcer file5

Control by buttons on the screen

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Control by mouse7

3.1. Render
3.2. Show Frame

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93.3. Fix clipping plane during rotation

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3.4. Connect view spaces

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3.5. Drawing Area Size

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3.6. Position
3.7. Scale Bar10113.8. Application

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4. "Tool" Menu

4.1. Save Screen Image

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4.2. Rotation

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5. Main Control

5.1. What is Unit?

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5.2. Operating Units

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5.3. Data Preference

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5.4. Voxel Export

175.5. Polygon Export

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System requirements / Contact us / Copyright18

3. "Preference" Menu

Additional Information

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1. Introduction
What is Molcer? What can it do for you?
What is 3D image viewer Molcer?
Molcer is software to view 3D objects.

FeaturesImportHalf or quarter size reading for huge data.

View
Show surface view of 3D objects (Surface Rendering).
Show penetrated view of 3D objects (Volume Rendering).
Show, hide and change rendering type and color by each unit (Main Control).
Show scale bar.
Easily control clipping plane to show section.
Rotate / Move / Scale 3D objects.
Show multiple 3D objects alongside, synchronize them.

ExportVoxel data export as a sectional image sequences (Voxel export)
Polygon data export with a STL / OBJ / glTF / glb format file (Polygon export)3

2. Basic Operation
How to open a Molcer file
There are four different ways to open the file;
Double-click the Molcer File (file extension;".mol").
Drag and Drop the Molcer File to the icon of Molcer application.
Start the Molcer application. Go to the "File" menu and choose "Open", then select Molcer File.
Start the Molcer application. Drag and Drop the Molcer File to the screen.

Open Sequential Images
Select "File (F)" > "Open Sequential Images (F)" in menu bar, and dialog below appears.

Press "Select Data", and open folder contains
sequential images, then choose one of them.
Press "OK" to draw 3-Dimensioned objects.
Available file format:
jpg, png, bmp, tif(8bit,16bit), DICOM. DICOM
without extension is also available. Data bitmust correspond when opening two data.

If "reverse image file reading order" is checked, sequential images are read by reversed order.
large number file
Sequential images

reverseorder

normalorder

small number fileIf sequential image in folder without size setting file selected, Data Preference dialog opens.
See "5.9 Data Preference" about Data Preference.

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Reverse order read object is drawn as mirror image.

Horizontal
MirrorImage

Vertical
Front / Back
MirrorImage

Mirrorreverse

Image

order

Rotateread

RotateOverwrite molcer file
Select "File (F)" > "Overwrite molcer file (W)" in menu bar, and you can overwrite molcer file only.

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Control by buttons on the screen

After opening a file, the screen right will be
displayed. All control buttons line up at thebottom, inside the white rectangle.

This is an enlarged image of thewhite rectangle interior. Eachbutton's explanation is described
below (function keys are also
usable).
(1) Home button(2) Rotation
buttons

Initialize 3D object's position to home. (F2 key)
Rotate 3D object clockwise (F3 key). / counterclockwise (F4 key).

(3) Whole/cut-off view switch button(F5 key)

Whole view

Whole object is shown.
Change to the cut-off view.

cut-off view

Cut-off object is shown.
Return to the whole view.

(4) Switch the control target during cut-off view button
target is object
target isclipping plane

You can control cut-off object. Section is fixed.
Target will change to clipping plane.
You can control clipping plane and change section. Object is fixed.
Target will return to object.

(5) Show/Hide Rotation Center button
Rotation Center is
not changeable(F6 key)(F7 key)

Rotation Center appears.

Rotation Centeris changeable

You can change Rotation Center by click.

(6) Delete button

Deletes the control target object when it is available.

Rotation Center hides.

(7) Animation
control buttons(8) Friend button

These buttons are available on time series
object. Animation playback, stop, pause andframe-by-frame.

When the button is available, the current object can switch to another one.
(F8 key)6

Control by mousewhole view / cut-off view (target is object)
Mouse can control whole or cut-off 3D objects: Movement, rotation, and scaling.
Rotate an object;
Press the left mouse button and drag the mouse. To continue the rotation, simply release the left mousebutton.
Rotate an object clockwise / counterclockwise;
To rotate clockwise, press and hold the left mouse button, and rotate mouse wheel forward.
To rotate counterclockwise, rotate mouse wheel backward.
Move an object up, down, left or right;
Press the right mouse button and drag the mouse. The object follows the drag movement.
To continue the movement, simply release the right mouse button.
Scale an object;
To enlarge an object, rotate mouse wheel backward.
To shrink the object, rotate mouse wheel forward.

target is clipping plane
While a 3D object is cut off and target is clipping plane, mouse can also control clipping plane.
Rotate clipping plane;
Press the left mouse button and drag the mouse.
To continue the rotation, simply release the left mouse button.
Move clipping plane vertically;
As rotate the mouse wheel, a clipping plane moves vertically.

Full screen display[F11] key can toggle full screen / normal display.

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3. "Preference" Menu
3.1. Render
To show Render Preference Dialog, select "Preference (P)" >"Render (R)" in menu bar.
You can change Molcer's render preferences by check boxes
and combo boxes.

cut front and back space ofrotation centerShow object cutting front and back space of rotation
center.
Set degree by [apply] combo box.

clip cover
Cover section of cut-off object. Voxel data would
be drawn if the object has it.
By "Unit Preference" in "Main Control", you caninvalidate this preference by a unit.

without covershadow
For more reality, you can attach some shadow to the 3D object.
Only available when "clip cover" is checked.
If you check "shadow", most objects have shadows. But some don’t.
Checking "shadow" may obviously reduce drawing speed.

8with coverdepth cues (fog)
If you check "depth cues"(sometimes called"fog"), you can see the objects as if in the fog(farther points fade into the background) .

without depth cueswith depth cues

without clipped areawith translucent clipped area

show clipped area translucently
Clipped area is drawn in translucent renderingtype.
By "Unit Preference" in "Main Control", you caninvalidate this preference or change drawing
method by a unit.

cut vertical and horizontal edges during connecting view spaces
Objects are shown with all edges cut when "Preference" > "Connect view spaces" menu is checked.
Select validity or degree by combo box.

projection
perspective;
The distance increases, the object is drawn smaller.
orthographic;
Object is drawn by constant size regardless of distance, , so you can easily see the object's height, widthand depth.

light position[upper right] [upper left] [lower right] [lower left] are available.

home button animation
Objects play animation when "Home button" is pushed. Select validity or speed by combo box.

3.2. Show Frame
A frame appears in the screen and helps to observe the 3D object, if "Preference (P)" > "Show Frame (F)"menu is checked.

93.3. Fix clipping plane during rotation
If "Preference (P)" > "Fix clipping plane during rotation (O)" menu is checked, object rotates alone whileclipping plane is fixed.
Without check, object and clipping plane rotate simultaneously.

3.4. Connect view spaces
If "Preference (P)" > "Connect view spaces (C)" menu is checked, all objects' motion in other view
spaces follow manipulation to the selecting object.

3.5. Drawing Area Size
Drawing area is between menu bar and control buttons.

heightwidth
To show Drawing Area Size Preference Dialog, select "Preference (P)"> "Drawing Area Size (A)" in menu bar.
Press "Apply" to set width and height by pixel.
"Width" and "height" are updated when real drawing area sizechanges.

3.6. Position
To show Position Preference Dialog, select "Preference (P)" >"Position (P)" in menu bar.
You can designate positions and angles of object and clipping
plane.
Press "Apply" button to apply input home and current values. Current
values are updated immediately as object or clipping plane moves.
Home values are used when "Home button" is clicked.
Press "Set Current Values to Home" button to overwrite home values
by current values.
"Screen coordinates" indicates mouse pointer’s position based on
coordinate system which has origin point at bottom left corner ofdrawing area.
Press "Save As File" button to save parameters to file. "Load File" torestore.

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"World coordinates" is expressed by coordinate
system that smaller axis ranges from -1 to 1, theother is normalized by smaller axis.

3.7. Scale Bar
To show Scale Bar Dialog, select "Preference (P)" > "Scale Bar (I)" inmenu bar.
"Frame size" indicates the length of one edge of the frame shown by"Preference" > "Show Frame" menu.
If you use "scale down in data reading" in "Preference" >"Application" menu, scale down ratio is shown.
Check "show" to show scale bar in the screen.

Move scale bar by inputting positionor pressing arrow buttons.
Usable scale units are: nm, um,
mm, cm and m.
Scale bar only appears when"projection" is "orthographic" in"Render Preference".

3.8. Application
To show Application Preference Dialog, select "Preference (P)" > "Application (Z)" in menu bar.
If your machine has not enough memory, occasionally memory errors occur.
Check the boxes of "scale down in data reading" to reduce load data size.
Press "OK" button and reopen the file.

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4. "Tool" Menu
4.1. Save Screen Image

Select "Tool (T)" > "Save Screen Image (S)" in menu bar, and you can capture screen and save it as a file.
Select folder, file format and input file name.

4.2. Rotation
To show Rotation Dialog, select "Tool (T)" > "Rotation (R)" in menu bar.

You can rotate objects by buttons on the dialog instead of mouse control.
Rotate by any degrees input in "angle" by one click.
If "90" box is checked, rotate by 90 degrees.

125. Main Control
5.1. What is Unit?
3D Object is consist of one or more parts.
The parts are called "Unit".
"Unit" has "Types" below.
"Voxel" :Voxel data drawn by volume rendering.

"Voxel Surface" :"Surface" :Voxel data drawn by surface rendering.
Polygon Surface generated from voxel data.

"STL" :

Polygon Surface generated from STL format file.

"Label" :Labeled Surface.

"Primitive" :Primitive Polygon.

and so on.

5.2. Operating Units"Main Control" shows list of all Units. You can change display / hide, name, rendering type and colorof the selected Unit. If you use "scale down in data reading" in "Application Preference", scale down
ratio is shown.
You can control display of Units by the check boxes on
the left. "Show All Units" and "Hide All Units" buttons cancontrol all check boxes at once.
Other items will be edited under the list to the selected
Unit.
[name] [rendering type] [opacity] [color] applies
immediately. "Back" button rewinds [color] to the lastone.
[opacity] is available when [rendering type] is B, C or D.
Buttons in "color of all units" box can control all Units'[color] at once. "Save" button to save, "Load" button toload.
"Voxel Surface" "Surface" and "STL" Units' surface aredrawn by assembly of triangles. [Rendering Types] arebelow.
A. Triangles are opaque.
B. Triangles are translucent.
C. Only triangles' vertexes are drawn translucently.
Triangles turning side are emphasized.
D. Only triangles' edges are drawn translucently.
Each triangle will be recognized.
E. A and D.

Enlarged view of "C"13

Enlarged view of "D"[Rendering Type] of "Voxel" Unit have three types below.
A. Colors are added from back to front (=alpha blending).
B. Use the largest value in added layers (=maximum intensity projection, MIP).
C. Color Transmission Map

5.2.1. Unit Preference (Surface, STL)
Press "Unit Preference" button in "Main Control" while selecting "Surface" or "STL" Unit, and dialog below
appears. This section combines explanation for same functions of "5.4. Unit Preference (Voxel Surface)".

"Forced turn off" in "clip cover" box invalidates designation in"Render Preference" for the selected Unit.
"Forced turn off" in "show clipped area translucently" boxinvalidates designation in "Render Preference" for the selected
Unit.
"Rendering type" and "opacity" specify drawing method ofclipped area.

5.2.2. Unit Preference (Voxel Surface)
Press "Unit Preference" button while selecting "Voxel Surface" Unit, and dialog below appears. See also
"5.3. Unit Preference (Surface, STL)" for some undescribed functions.
Press "Apply" button after inputting "upper
limits" or "lower limits" to change
isosurface value range.
You can also change "lower limits" or"upper limits" by dragging bars on
histogram graph shown on the left.
"Upper limits" is green bar and "lower
limits" is red bar.
Press "Reset" button to abandon allchanges.
Histogram graph of voxel value is shown on the left.
Graph height is normalized by maximum frequency value.
Usable magnifications range from one to one million.
Press "Export Histogram" button to export histogram values to a text file.

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You can set pseudo color on section by [Section Color]. Select one ofthree color scales. Section will be colored.
Press "Auto Set" to adjust "maximum" and "minimum" value to"upper limits" and "lower limits" respectively.
See "5.9. Data Preference" about "Data Preference".

5.2.3. Unit Preference (Label)
Press "Unit Preference" button in "Main Control" while selecting "Label" Unit, and dialog below appears.
You can change each label color.
Press "Export Histogram" button toexport histogram values to a text file.
See "5.9. Data Preference" about "Data
Preference".

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5.2.4. Unit Preference (Voxel)
Press "Unit Preference" button in "Main Control" while selecting "Voxel" Unit, and dialog below appears.
Histogram graph of voxel value is shown on theleft.
See also "5.4. Unit Preference (Voxel Surface)"
about histogram.
You can change "brightness", "contrast", "lower
and upper limits of voxel value" freely.
You can also change "lower and upper limits ofvoxel value" by dragging bars on the histogramgraph.
Press "Reset" button to abandon all changes.

5.2.5. Unit Preference (Voxel Color Transmission Map)
Press "Unit Preference" button in "Main Control" while
selecting "Voxel" Unit whose "rendering type" is C, anddialog right appears.
This dialog provides transmission map settings. See also
"5.4. Unit Preference (Voxel Surface)" for someundescribed functions.
"limits of voxel value"
Set by three horizontal slide bars below, upper, middle andlower. Slide bars move in the range that do not violate theorder, lower <= middle <= upper. You can also designate
each voxel value by inputting.
"opacity maximum"Set by vertical slide bar right. You can also designate value
by inputting.
"color"Select one of three color scales by combo box. Designate "maximum" and "minimum" value by inputting.
Press "Auto Set" button to adjust "maximum" and "minimum" value to the unit respectively.

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5.2.6. Unit Preference (other)Press "Unit Preference" button in "Main Control"
while selecting Unit other than "Voxel Surface""Voxel" "Surface" "STL" "Label", and dialog likeright appears corresponding to "Type".
Changes by combo box or check box apply
immediately.
You can edit values in right area by selecting
list. Pressing "Apply to List" button updates
values.

5.3. Data Preference
Press "Data Preference" button on "Unit Preference" dialog of"Voxel Surface" or "Voxel" Unit, and dialog right appears.
If you use "scale down in data reading" in "Application
Preference", scale down ratio is shown.
"Size" in "voxel information" box indicates number of voxels forx-, y- and z-axes.
You can manipulate resolutions for each x-, y- and z-axis.
Usable scale units are: nm, um, mm, cm and m.

Press "Data Preference" button on "Unit Preference" dialog of"Surface" or "STL" Unit, and dialog right appears.
"Coordinates range" indicates minimum and maximum values ofpolygon surface data for x-, y- and z-axes.
Usable scale units are: nm, um, mm, cm and m.

5.4. Voxel Export
Press "Voxel" button in "export file" box of Main Control, and dialog below appears.
You can export sectional image sequences with specified corresponding voxel values.
Press "OK" button and select save folder.

5.5. Polygon Export
Press "Polygon" button in "export file" box of Main Control, and dialog below appears.
You can export polygon data with specified file format (STL, OBJ, glTF and glb are available) andmagnification.
Press "OK" button and select save folder and save file.

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Additional Information
System Requirements
Windows 7 / 8 / 10
1GB of system memory (4GB recommended)
Graphic card that supports OpenGL 3.3 or higher

Contact us
We are waiting for your comments, wishes, bug findings etc...
Please email;support@white-rabbit.jp
If you inform us of bugs, please add the detailed situation of the error that had occurred.
You can see the latest version of our programs on our website;
https://white-rabbit.jp/en/

Copyright
This software is free to use.
The copyright holder is White Rabbit Corporation.
This software is protected by the copyright laws and by international treaty provisions.
You shall not reprint the Software.
You may not reverse engineer, decompile, disassemble or any other attempts to discover thesource code of the Software.
You may not modify the part or whole of the software and attached documents.
EXEMPTION CLAUSE; We are not liable for any damage or injury caused by using our products.
The 3D Rabbit model used in this manual is :Stanford Bunny
https://graphics.stanford.edu/data/3Dscanrep/(c)Stanford Computer Graphics Laboratory
The 3D Deep-Sea Fish model used in this manual is :3D-CT Deep-Sea Creatures (Japanese)
https://www.aori.u-tokyo.ac.jp/project/3D/index.html

White Rabbit Corporation
Tokyo, JAPANE-mail: info@white-rabbit.jp
https://white-rabbit.jp/en/

White Rabbit

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