Is there manual crop module?

Image Analysis
#1

Hi,

Is there manual crop module? Because I want to deal with totally different images.
I also looking modules that can adjust the objects after the IdentifyPrimAutomatic, for example, delete objects or include objects from the background.
Please tell me if there is reasonable way to modify throughout all this image process.

Thanks a lot.

Wenhuo Hu

#2

Hi,

There is no manual crop module, but there are options to crop each image differently using the Crop module. You can crop each image into objects identified within that image, for example (which would scale to the size of the image) or to a corresponding template that you’ve loaded. You can also manually outline an ellipse or rectangle to crop for each image, by selecting either Ellipse or Rectangle (rather than a specific object) as the shape you would like to crop into, then selecting Mouse as the option for how you would like to crop. Finally, make sure to select Individual for how you the cropping pattern should be applied. In this mode, you will be presented with each image and you get to click around to define the cropping shape.

A similar method of manual identification is possible using IdentifyPrimManual. Every cycle, you are presented with the image and can click around to define the objects.

As of now, there is no easy way to go from objects automatically identified in IdentifyPrimAuto to adding or deleting them, as you suggest (though we’ve had other requests!). You can certainly convert your objects to an image, for example, then outline each one that you’d like to keep manually in IdentifyPrimManual- but adding objects is a bit trickier. It’s best to just start from manual segmentation in that case.

~kate

#3

Thanks Kate.

How can I manually outline an ellipse in cellprofiler? Another question is when using identifyprimmanual, is there anyway I can select object by one click per object? It may not identify the exact rim of the cell, but I think it is cool when only for counting cell number. And how to do manual segmentation?

Wenhuo Hu

[quote=“klmadden”]Hi,

There is no manual crop module, but there are options to crop each image differently using the Crop module. You can crop each image into objects identified within that image, for example (which would scale to the size of the image) or to a corresponding template that you’ve loaded. You can also manually outline an ellipse or rectangle to crop for each image, by selecting either Ellipse or Rectangle (rather than a specific object) as the shape you would like to crop into, then selecting Mouse as the option for how you would like to crop. Finally, make sure to select Individual for how you the cropping pattern should be applied. In this mode, you will be presented with each image and you get to click around to define the cropping shape.

A similar method of manual identification is possible using IdentifyPrimManual. Every cycle, you are presented with the image and can click around to define the objects.

As of now, there is no easy way to go from objects automatically identified in IdentifyPrimAuto to adding or deleting them, as you suggest (though we’ve had other requests!). You can certainly convert your objects to an image, for example, then outline each one that you’d like to keep manually in IdentifyPrimManual- but adding objects is a bit trickier. It’s best to just start from manual segmentation in that case.

~kate[/quote]

#4

Manual segmentation of any object (ellipse or otherwise) is performed the same way with IdentifyPrimManual: Clicking the outline of the proposed object in order to delineate it. If you want to create an elliptical object, you will have to approximate the outline with mouse clicks. Unfortunately, there is no way to select an object with one click, although that ability is certainly a feature to add in the future.

Regards,
-Mark

#5

Manual cropping is now available within the Crop module.
-Mark

#6

i have a problem in drawing a rectangle manually…
I can click around, nothing happens, it just uses the predefined rectangle.
Both with the lates MacOSX and windows version.
Am I missing something?=

#7

Please make a new thread with the information we request for diagnosing an issue. Are you actually still using CP 1.0?

#8

Well its alright.
I think the main point is that CP is not for making new images but rather to analyze.
I ll go for IJ before analysis
thanks RB

Robert Brunkhorst
Ludwigstr. 74
63067 Offenbach am Main
Tel.: 0176/63605777

robert.brunkhorst@gmail.com

#9

Hi guys,

is there a way to fix the window size of manual (mouse) cropping? It would be great to enter fix coordinates and just moving around the window. At this step a scale bar option would be awesome too.

Many thanks for the great work!
Florian

#10

Hi @Florian_Deckert,

In the Crop module, You could enter the coordinates. But no sure though if it automatically recognise coordinates with respect to the mouse pointer.

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
For CellProfiler training or optimised pipeline write to,
lakshmi.balasubramanian.contractor@fujifilm.com

Read more on our site.
Yokogawa CV8000 - The Ultimate in Confocal HCS
https://www.wakoautomation.com/products/yokogawa-high-content-imaging

Join us at, https://www.slas2020.org