New plugin for easily accessing image series

Announcements
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#1

Dear all,
I just released a new plugin that uses Bio-Formats to easily browse and open image series contained in files that can hold multiple images, like *.lif, *.czi or others.
The plugin can be obtained by activating my IBMP-CNRS Fiji update site.
For ImageJ1 users, you can get the RML_.jar file directly from Index of /Mutterer/plugins but you’ll also need the latest ActionBar from the same location, and latest BioFormats jar file ( Download (31.64 MB)).

  • Start “Read My Lifs” and you’ll be presented with a small window.
    image
  • You can drag and drop LIF or CZI files on it, which will create an image stack with thumbnails of all series in that file. You can leave this small window open, scroll through it, and open any series by double clicking on the thumbnail.
  • This saves you from either opening all series, which can bloat your workspace, or having to repeatedly go through the bioformats options and/or series dialog.

I hope you find this useful!.

Please use this thread to post comments and discuss issues.

Jerome.

7 Likes
#2

A first issue is the name…
I first wrote this plugin to tackle the issue I had of repeatedly having to go through the bioformats series dialog for my *.lif files, hence the “Read My Lifs” name.
Within an hour of release, @sebi06 pointed out that the plugin was of more general use, for example for *.czi files that can also contain multiple images (or ‘series’). Indeed the plugin simply worked on CZI files without modification, by just allowing czi file extension. I reflected this on the logo, but the same will happen with other formats like .nd2 or others.

I’d suggest to leave the name like this for now because it’s easy to remember for new users, but I’m happy if someone comes up with a new generic name and logo. The released “Read My Lifs” name could still be used as an alias, so early adopters wouldn’t notice the change.

Jerome.

1 Like
#3

:heart: for migrating the discussion here! Was trying to figure out how to respond to https://twitter.com/haesleinhuepf/status/1354010348806930432 in 280 characters.

You mentioned:

So I guess my question would be: does anything need porting back to #bio-formats or is the usability/friendliness as a plugin fine for most/all?

3 Likes
#4

Hi @jerome

thanks for the great idea. I am running fiji (up-to-date) on linux(arch) and after dropping a bunch of czi files on the window all it does is open them and add a header below. I ended up with 20 small windows open instead of one that I can browse through. No error messages on the console.
I try to help if you let me know how.

#5

Hi Josh!
Thanks for asking that, I had not thought of it this way.
I’m not sure how others are using BF, so I wouldn’t have asked for significant changes in the existing UI.
But this plugin would indeed be redondant if the BF series dialog were non modal, more compact, and if double clicking its thumbnails would open the corresponding series.

Another point is skipping the options dialog. This can partially be achieved already using the windowless option in BF configuration, but then the series dialog is also skipped, and only the first image can be read in this mode. Also when you ever need to change the default options, it’s nice to have them by simply using the Bio Format Importer command.

From the nice community response the plugin announcement had on twitter, I’m sure people would love to have these features directly in BF if possible.

Jerome.

2 Likes
#6

That’s the intended behaviour: each file yields a stack with images series that it contains.
Do your CZI files each contain multiple image series?

1 Like
#7

In this post, @sebi06 highlights a calibration issue with pyramidal CZI files. I can try to look into it thanks to the provided working code example, but it’s more likely to be a Bio-Formats issue for @joshmoore

#8

@jerome, let me know if you want me to split that issue into a separate topic. ~J.

#9

Hi all,

I am not so sure, if this is really a BF issue, it is rather a missing feature :-). If one decided to open a CZI with pyramid levels, the scale of the resulting image is not automatically adapted depending on the level. The correct scaling for pyramid levels is of course inside the CZI metadata, but is mots likely not used so far.

This is why I update the scaling after the read the CZI via the script from above. Sure it would be cool to have BF read the pyramid levels including the correct scaling.

1 Like
#10

thank you for the plugin!
It could be really useful,
I was just noticing that this way of opening creates an issue if you want to zoom the image…
I was zooming it and it understood it as a double-click and opened the series :wink:

#11

Thank you @emartini for the report. I’m a slow-zoomer and didn’t notice that but you’re right.
Here what I suggest for the next version:
If you have the zoom tool selected, double clicking brings a status message warning that you must use SPACE+double click to open the series, or change tools.
Would that be OK for your use case?

Jerome.

1 Like
#12

I really think it will work fine,
thank you for the consideration

#13

This plugin is a cool idea!
However, when I tried to open .czi images of a certain size by drag&drop, I keep getting the following error message:
LIFs_error_message

I have pyramid images acquired with an Axio Scan Z1 slide scanner. Data size ~1.5-2 GB
The 10x scans of the same scanner open without problems.

Is this a known problem?

*edit: It is not possible to open the series with the highest resolution in Fiji. But starting from the second series, it works

#14

Thanks for trying it!
Can you open the same file using Plugins>Bio-Formats>Bio-Formats Importer ?

Jerome

#15

Sorry. Yes I forgot to mention that in the first post and added an *edit
No it’s not possible to open the series with the highest resolution, but starting from the second-highest, bioformats can open the images

1 Like
#16

Salut Jérôme,
Cool ! Thanks a lot for that plugin ! tried it in Fiji like a beotian and I have small question : I needed to remove my Bioformats.jar coming from the Bioformat updates (error message of duplicate versions as expected) : is your version will be updated like the Bioformat update?
Amicalement,
Frédéric

#17

Salut Fred!
This plugin depends on BioFormats but does not include it. So you need to activate both IBMP-CNRS and Bio-Formats Fiji update sites. I think it’s usually best not to add/remove jar files manually from the plugins folder. What’s the error message you’re getting?

Jerome.

1 Like
#18

Never read manual before use. I somehow didn’t read the instructions careful enough and had the idea that the plugin would do the inverse namely combine a bunch of czi files into a stack for a quick preview of an entire folder.

sorry for the confusion

Gregor

1 Like
#19

Salut Jérôme,
Ok, sorry… I added the bioformat folder you proposed to download and removed the updated one from Fiji, as I thought from your explanation that it was the package needed… So, everything is ok if you just ask for your IBMP installation/updates and keep the Bioformat updates in Fiji.
A+
Frédéric

1 Like
#20

For visually browsing microscopy image folders, I’d recommend FocalPoint by Simon Andrews. It hasn’t been updated in a while, but still works for me, including for CZI files I tested.

http://www.bioinformatics.babraham.ac.uk/projects/focalpoint/