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Fiji Cookbook and hyperstacks

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Christine Labno-2

Fiji Cookbook and hyperstacks

A subject line would be nice. . . sorry.

Hello Fiji Cookbook folks and other Listhost-ers,

Do the tools of the Fiji Cookbook, specifically the T-functions tools, work on single channel, Z + T hyperstacks? That is, how can I be sure I'm getting Z1T1 - Z1T2 vs. Z1T1 - Z2T1?

This may be a dumb question, but I've searched the (otherwise very nice) documentation and I can only find info on 3D (XY over time) data, not 4D (XYZ over time) data.

Thanks!
Christine

--------------------------------------------
Christine Labno, Ph.D.
Asst. Technical Director
Light Microscopy Core
University of Chicago
Office of Shared Research Facilities
KCBD 1250 900 E. 57th St.
(773) 834-9040 (phone)

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ctrueden

Re: Fiji Cookbook and hyperstacks

Hi Christine,

> Do the tools of the Fiji Cookbook, specifically the T-functions tools,
> work on single channel, Z + T hyperstacks? That is, how can I be
> sure I'm getting Z1T1 - Z1T2 vs. Z1T1 - Z2T1?

I checked the source code for Delta F Up and Delta F Down:
https://github.com/fiji/cookbook/blob/master/cookbook_/src/main/java/Delta_F_up.java
https://github.com/fiji/cookbook/blob/master/cookbook_/src/main/java/Delta_F_down.java

It seems your suspicions are well founded: Delta F Up works across all
slices of the image, regardless of dimension, so for 4D data it will not
work as expected. And worse (arguably): Delta F Down is not even
implemented! Its for loop is empty.

I filed two new bug reports tracking these issues:
https://github.com/fiji/cookbook/issues/3
https://github.com/fiji/cookbook/issues/4

The code is not too complicated, so if you have time and knowledge to fix
it (submitting patches as a GitHub Pull Request:
https://help.github.com/articles/using-pull-requests) that would be
awesome. Or if not, we will try to fix as our time allows—but very likely
not before mid-June.

Regards,
Curtis

On Thu, May 15, 2014 at 12:51 PM, Christine Labno <[hidden email]>wrote:

> A subject line would be nice. . . sorry.
>
> Hello Fiji Cookbook folks and other Listhost-ers,
>
> Do the tools of the Fiji Cookbook, specifically the T-functions tools,
> work on single channel, Z + T hyperstacks? That is, how can I be sure I'm
> getting Z1T1 - Z1T2 vs. Z1T1 - Z2T1?
>
> This may be a dumb question, but I've searched the (otherwise very nice)
> documentation and I can only find info on 3D (XY over time) data, not 4D
> (XYZ over time) data.
>
> Thanks!
> Christine
>
> --------------------------------------------
> Christine Labno, Ph.D.
> Asst. Technical Director
> Light Microscopy Core
> University of Chicago
> Office of Shared Research Facilities
> KCBD 1250 900 E. 57th St.
> (773) 834-9040 (phone)
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Christine Labno-2

Re: Fiji Cookbook and hyperstacks

Hi Curtis,

Thanks for looking in to that so quickly. I'm not sure my coding skills are strong enough to fix the bug, but I think I can at least find a work around for the Delta F Up.

Best,
Christine
--------------------------------------------
Christine Labno, Ph.D.
Asst. Technical Director
Light Microscopy Core
University of Chicago
Office of Shared Research Facilities
KCBD 1250 900 E. 57th St.
(773) 834-9040 (phone)

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Curtis Rueden [[hidden email]]
Sent: Thursday, May 15, 2014 1:27 PM
To: [hidden email]
Subject: Re: Fiji Cookbook and hyperstacks

Hi Christine,

> Do the tools of the Fiji Cookbook, specifically the T-functions tools,
> work on single channel, Z + T hyperstacks? That is, how can I be
> sure I'm getting Z1T1 - Z1T2 vs. Z1T1 - Z2T1?

I checked the source code for Delta F Up and Delta F Down:
https://github.com/fiji/cookbook/blob/master/cookbook_/src/main/java/Delta_F_up.java
https://github.com/fiji/cookbook/blob/master/cookbook_/src/main/java/Delta_F_down.java

It seems your suspicions are well founded: Delta F Up works across all
slices of the image, regardless of dimension, so for 4D data it will not
work as expected. And worse (arguably): Delta F Down is not even
implemented! Its for loop is empty.

I filed two new bug reports tracking these issues:
https://github.com/fiji/cookbook/issues/3
https://github.com/fiji/cookbook/issues/4

The code is not too complicated, so if you have time and knowledge to fix
it (submitting patches as a GitHub Pull Request:
https://help.github.com/articles/using-pull-requests) that would be
awesome. Or if not, we will try to fix as our time allows—but very likely
not before mid-June.

Regards,
Curtis

On Thu, May 15, 2014 at 12:51 PM, Christine Labno <[hidden email]>wrote:

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Pariyt83

Re: Fiji Cookbook and hyperstacks

In reply to this post by Christine Labno-2

Hello friends! I am looking for some online cooking classes to learn Thai food. I love cooking but I am not familiar with traditional Thai food recipes. I wonder if anyone can help me!!