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Examples
Marking
and categorizing oocytes
Version 27
01-apr-2010 vischer at science.uva.nl
This project allows automatic and manual measurements of
oocyte cells.
Resulting parameters are cell size and elliptical aspect
ratio. Size
is visualized by a red line indicating the diameter of
equivalent circle with same area.
A category (1..9) can be added manually, and is visualized
by the "hand of a clock".
You can get statistics of any subset of objects that meets a
combination of properties
Watch the movie
A - Install ObjectJ
1. Download
ObjectJ from https://sils.fnwi.uva.nl/bcb/objectj/
go to "download" and choose
the version with the
highest number, currently ObjectJ 1.01n)
2. put
objectj_.jar into the plugins folder of the ImageJ folder
3. Restart
ImageJ
4. choose
menu Plugins>ObjectJ
5. Now
the menu bar should show "ObjectJ" (between "Analyze" and
"Plugins")
6. (Next
time, ObjectJ can be upgraded simultaneously with ImageJ
via: menu Help>Update ImageJ)
B - Download Sample Project
1. Download
oocytes-27
(version number may be higher)
Folder contains:
project file= oocytes-27.ojj
Anchovy_oocytes.jpg
Fec 5.jpg
2. Make
sure these files are in the same folder
after unpacking, we call it the
"project folder". You can replace
the sample image by any number of your
own images
3. Drag
the .ojj file into the ImageJ main window to
open this project, wait until the
project window
appears showing the names of "Linked
Images"
(Alternatively, choose menu
ObjectJ>Open Project..).
C - Usage
1. Automatic marking
of diameters
-
chose menu ObjectJ>Mark Oocytes...
- In the dialog, if threshold is set to
zero, you are asked to
threshold each image interactively.
2. Categorize any marked cell
- With
no Roi visible, locate the cursor above a marked cell and press
key
1..9 for category. Cell will obtain that category as hand of a clock
(e.g.
4 o'clock is category 4), - or cell will
be
killed if 0 is pressed. (You also could kill a cell
with
the pistol tool).
3. Label cell
only without measuring it
A a line of
fixed length (185 um at 45 deg) is used to
mark
the existence of a cell type.
- Choose
menu ObjectJ>Fixed Diameter [F] (or select
the
"F" button in the ObjectJ tools window).
Then,
click on the center of a cell to mark it.
4. Show/Hide floating
circle
A floating
circle that follows the cursor movement
can
help to visually estimate cell sizes. It's diameter is 185 um.
- Choose ObjectJ>Variable Diameter (toggle
circle) [V],
or
press "V" key.
This
activates the "V" tool in the ObjectJ Tools window;
and
switches the floating circle on or off. If the mouse rests for
10
sec, the floating circle will be switched off.
You
can press V again to switch it on again.
5. Show/Hide Ellipses
Shows or hides the
ellipse items of marked cells.
6. Manually marking of
ellipses:
- make
sure the variable ellipse tool (button marked with "V") in ObjectJ
Tools is selected
- click
and drag along a line A-B to follow the ellipse major axis (or
diameter
in case of a circle).
After
releasing the mouse, a circular roi is shown.
- if
you want to leave this circular roi as such,
move
the cursor further outside until the roi flashes
- otherwise,
if you want to change the circle into an ellipse, then move the cursor back
inside,
which decreases the minor axis. During this phase, you also can
fine-adjust
the orientation.
Now
you need a second mouse-down click to confirm the current ellipse.
Before
again releasing the mouse button, you can re-adjust the ellipse's position.
- At
any moment during ellipse editing, you can press any category key (1..9)
to
finalize and categorize the ellipse.
7. Convert ellipse roi
into marked and categorized cell
- when
an elliptical roi is visible, it can be marked and categorized with
key
1..9. After that, the "V" tool remains activated.
8. Categorizing
marked cells sequentially:
This
mode is intended to visit marked cells in sequence (1, 2, 3..),
in
order to categorize them.
- The
sequential modus is active when a
halo visible. The halo is
symbolized
by two concentric rois.
The
inner roi corresponds to the diameter of the selected cell, the
outer
roi is used for "zoom to selection"
- You
can enter the sequential modus by locating the cursor
above
a marked cell (e.g. cell 17) and press the "Q" key, that corresponds
to
Toggle
Sequential Mode [Q]
The
halo now highlights cell 17
(If
the halo was already active, it will disappear)
- With
the halo visible, press any key 1..9 to categorize that
cell,
or press zero to kill it.
After
0.25 sec, the halo highlights the next cell (cell 18 in the example).
- Use previous [p] or next [n] shortcuts to navigate the
halo.
9. Applying
a default category
- You
can set a default category to all objects that have no category yet.
This
is done in all linked images.
- Choose
ObjectJ>Categorize all uncategorized cells...
and
after entering a number, all uncategroized cells will be categorized.
10. Results
- Choose
ObjectJ>Show Project Results
to
display numeric results. These columns are implemented:
Dia equivalent
diameter in um
Cat
category
1..9
Roundn. same as Minor/Major (range 0..1)
Ellipt. ellipticity=
ellipse perimeter/actual perimeter
(range
0..1, or empty for manual marking)
Minor minor axis (um)
Major major axis (um)
Area3 area (unit is
10^3 um^2 for convenience)
11. Saving
- Periodically
save the colored markers via menu ObjectJ>Save project.
(Note
that menu "File>Save" only saves an image, not the markers)
12. Mark
your own images
- once the described sample
project works satisfactory, you can save an empty copy
of the project file via ObjectJ>Project
File> Save an Empty Copy… and
relaunch ImageJ.
- The empty copy contains all internal
structure and macros, but no markers or linked images.
- Link your images via ObjectJ>Linked Images> Link Image
from project Folder
- Make sure your linked images are
scaled correctly (eg pixels per um)
13. Notes
- cells with fixed diameters don't
have any quantitative result entries.
- category 0 cannot be applied, it is
rather used to delete an object under the cursor
- marking a cell with "fixed
diameter" does not invite to add a category
- Categorize all unmarked cells also
categorizes those with fixed diameter