Search field on menu

imagej
neubias
#21

hello, @vcaldas and @haesleinhuepf ,
here is a text example of json export, enabled on the TEST version (do not tag anything here it would be lost):
http://test.biii.eu/searchjsonexport?search_api_fulltext=neuron&_format=json
where neuron has to be replaced by your request.
It would return a json file to be parsed:
such as

[{"title":"nctuTW","search_api_relevance":"5"},{"title":"ORION ","search_api_relevance":"4"},{"title":"neuTube (or NeuTu)","search_api_relevance":"3"},{"title":"MeasureNeurons","search_api_relevance":"3"},{"title":"NBLAST","search_api_relevance":"3"},{"title":"Neurolucida","search_api_relevance":"3"},{"title":"NeuronStudio","search_api_relevance":"3"},{"title":"APP (All-path pruning)","search_api_relevance":"3"},{"title":"CREMI challenge","search_api_relevance":"3"},{"title":"NeuriteTracer","search_api_relevance":"2"}]

If you want two terms, add + (e.g. neuron+segmentation), or & (e.g neuron&segmentation) if you want to search for one word or/and another one. We can add whatever field has requested, let me now your requirements. SUch as the description summary, the dependencies (the platform required , the type (collection, component, workflow) links…, operation performed, topics, etc…

Does it help?

Please note that the example is anble on test.biii.eu, if you validate, I will add it on the next version that will be deployed this week.

PS:
for all: Just a reminder that you can follow NEUBIAS as well in FIJI in update sites: https://github.com/NeuBIAS/neubias-ijsearch, should we merge the two source repositories in one?

2 Likes

#22

Hey @PerrineGilloteaux,

that sounds great! I’m happy to incorporate that in the BISE-search.

Regarding the repository merging: That might not be necessary as scijava-search is part of core-Fiji. Thus, everybody would get access to BISE without the need to install an update site. I think that has huge potential. I’m sorry that I didn’t manage to communicate that 14 months ago, when the search-bar was invented. Now we’ll manage it :wink:

Thanks for your support!

Cheers,
Robert

1 Like

#23

This would be super great , many thanks for this . What is the wish list ? Title, url link to the Entry full description in bise , dependencies ( e.g Fiji, cell profiler , icy…) ; operation performed ( tags based on Edam bio imaging ontology) ; summary description OR full text description ? More fields ? Less fields ? And then people click on the link to know more ?

1 Like

#24

I’d say title, short description and link are minimum. The rest is up to you or up to the community to decide. I personally would love to get a link to the thumbnail image :wink:

0 Likes

#25

Let’s start with this for test and new version : title, link , summary , thumbnail, and then let’s wait for feature request !

1 Like

#26

Hey @PerrineGilloteaux,

there we go:
image

FYI the code lives here for the moment:
https://github.com/haesleinhuepf/scijava-search/blob/master/src/main/java/org/scijava/search/web/BISESearcher.java

I guess the API on server side needs to be extended to deliver title, link , summary and thumbnail? Or is there some additional parameter I have to hand over to get them?

Thanks for your support!

Cheers,
Robert

3 Likes

#27

Hi Robert, you are right I need to update them; I just wanted to check with you if the format was ok this time , I m waiting my pull request to BISE to be accepted , in which I will add these features . I will ring the bell here when ready. Thanks a lot!

2 Likes

#28

For the record (and for others interested in the matter), here’s the PR you mentioned:

1 Like

#29

Hi Jan,
Not yet :slight_smile: this one is not related (I am working on a new branch for this and other updates)

1 Like

#30

In any case, not versionned yet, here is the way it loonks witrh description and thumbnailm images, could you check if format is ok?

[{"title":"nctuTW","search_api_relevance":"5","body":"\u003Cp\u003EnctuTW is a \u0022high-throughput computer method of reconstructing the neuronal structure of the fruit fly brain. The design philosophy of the proposed method differs from those of previous methods. We propose first to compute the 2D skeletons of a neuron in each slice of the image stack. The 3D neuronal structure is then constructed from the 2D skeletons. Biologists tend to use confocal microscopes for optimal images in a slice for human visualization; and images in two consecutive slices contain overlapped information.","field_image":"\/sites\/default\/files\/styles\/thumbnail\/public\/2017-09\/journal.pcbi_.1002658.g005.png?itok=vCIyCDoF"},{"title":"ORION ","search_api_relevance":"4","body":"\u003Cp\u003EORION: Online Reconstruction and functional Imaging Of Neurons: segmentation and tracing of neurons for reconstruction.\u003C\/p\u003E","field_image":"\/sites\/default\/files\/styles\/thumbnail\/public\/2017-09\/ORION.png?itok=npiWPQ3u"},{"title":"NBLAST","search_api_relevance":"3","body":"\u003Cp\u003EThis R package implements the NBLAST neuron similarity algorithm described in a preprint available at \u003Ca href=\u0022http:\/\/dx.doi.org\/10.1101\/006346\u0022\u003Ehttp:\/\/dx.doi.org\/10.1101\/006346\u003C\/a\u003E. In addition to basic pairwise comparison, the package implements search of databases of neurons. There is also suport for all x all comparison for a group of neurons. This can produce a distance matrix suitable for hierarchical clustering, which is also implemented in the package.\u003C\/p\u003E","field_image":"\/sites\/default\/files\/styles\/thumbnail\/public\/2018-01\/nblast.png?itok=WyFpbbQF"},{"title":"Neurolucida","search_api_relevance":"3","body":"\u003Cp\u003ENeurolucida is a powerful tool for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. Perform detailed morphometric analysis of neurons, such as quantifying 1) the number of dendrites, axons, nodes, synapses, and spines, 2) the length, width, and volume of dendrites and axons, 3) the area and volume of the soma, and 4) the complexity and extension of neurons. See 10.3389\/fnins.2012.00049\u003C\/p\u003E","field_image":"\/sites\/default\/files\/styles\/thumbnail\/public\/2017-09\/stan_CLARITY_0.PNG?itok=vVNmw5OK"},{"title":"NeuronStudio","search_api_relevance":"3","body":"\u003Cp\u003ENeuron studio is a software package to reconstruct neurons from 3D confocal images. Reconstruction can be done manually, semi-manually or fully automatic. The images as well as the detected objects are rendered in 3D. A spine detection and classification function is also included. Results can be exported as a text file with coords of the spines. It seems that active development has stopped in 2009.","field_image":"\/sites\/default\/files\/styles\/thumbnail\/public\/2017-09\/ns.png?itok=LuoOXfoW"},{"title":"APP (All-path pruning)","search_api_relevance":"3","body":"\u003Cp\u003E\u0022We have developed an automatic graph algorithm, called the all-path pruning (APP), to trace the 3D structure of a neuron. To avoid potential mis-tracing of some parts of a neuron, an APP first produces an initial over-reconstruction, by tracing the optimal geodesic shortest path from the seed location to every possible destination voxel\/pixel location in the image.","field_image":"\/sites\/default\/files\/styles\/thumbnail\/public\/2017-09\/APP.PNG?itok=ym8j3EpA"},{"title":"CREMI challenge","search_api_relevance":"3","body":"\u003Cp\u003EMICCAI Challenge on Circuit Reconstruction from Electron Microscopy Images\u003C\/p\u003E","field_image":"\/sites\/default\/files\/styles\/thumbnail\/public\/2018-01\/cremi_examples_AB.png?itok=jc89Gb-i"},{"title":"neuTube (or NeuTu)","search_api_relevance":"3","body":"\u003Cp\u003EneuTube is a collection of neuron reconstruction tools from fluorescence microscope images. It has an interactive system with a 3D viewer, which can be clicked in 3D and perform neuron tracing automatically and semi-automatically. It can automatically recognize branching points as junctions. Traced neurons can be exported to swc format, which could be imported by various software packages. neuTube has Win and Mac OS standalone executable builds and may also be installed by manual compilation. In addition, neuTube can be used as a plugin in Vaa3D.\u003C\/p\u003E\n\n\u003Cp\u003E\u00a0\u003C\/p\u003E","field_image":"\/sites\/default\/files\/styles\/thumbnail\/public\/2017-09\/neutube_0.PNG?itok=Wrsahzt_"},{"title":"MeasureNeurons","search_api_relevance":"3","body":"\u003Cp\u003EThe forum discussion below might be of interest. Sample cppproj files are available in the discussion.\u003C\/p\u003E\n\n\u003Cp\u003E\u003Ca href=\u0022http:\/\/forum.cellprofiler.org\/t\/creating-a-pipeline-to-measure-neurons\/4750\u0022\u003EMeasure Neurons - Total Neuron Length Measurement\u003C\/a\u003E\u003C\/p\u003E\n","field_image":"\/sites\/default\/files\/styles\/thumbnail\/public\/default_images\/NEUBIASlogo.png?itok=pvuUqhrP"},{"title":"Simple Tracing DF-Tracing ","search_api_relevance":"2","body":"\u003Cp\u003EWe have developed a novel approach, named DF-Tracing, to tackle this challenge. This method first extracts the neurite signal (foreground) from a noisy image by using anisotropic filtering and automated thresholding. Then, DF-Tracing executes a coupled distance-field (DF) algorithm on the extracted foreground neurite signal and reconstructs the neuron morphology automatically.","field_image":"\/sites\/default\/files\/styles\/thumbnail\/public\/2017-09\/Simple%20Tracing%20-%20DT-field.PNG?itok=OyduR4hA"}]
1 Like

#31

in the example above (http://test.biii.eu/searchjsonexport?search_api_fulltext=neuron&_format=json once again just for testing purpose, it will be desactivated soon) , the prefix to be set before /sites/default etc… is test.biii.eu. Also for now I ve trimmed the description to 600 chars, could be less, could be more.

1 Like

#32

Oh, sorry. It was the only PR open on bise, and you said you’re waiting for it to be accepted, so I though it can only be this one… :slight_smile:

1 Like

#33

Hey @PerrineGilloteaux,

looks better now. :slight_smile:
image

However, I’m wondering, how is the link supposed to be assembled and from what?

Thanks again!

Cheers,
Robert

2 Likes

#34

So for link to the entry directly: i did not Added it since it should be biii.eu/title such as http://biii.eu/nctuTW or http://biii.eu/simple-tracing-df-tracing (rule: space are replaced by -.

For the link to the thumbnail, just add biii.eu before such as http://biii.eu/sites/default/files/styles/thumbnail/public/2017-09/Simple%20Tracing%20-%20DT-field.PNG?itok=OyduR4hA

Did I answer your question?

1 Like

#35

Yes. I need to find out how to make the search window load the thumbnails. But I’m optimistic that this works.

Ring the bell when your PR was accepted, I will then submit mine :wink:

Thanks again for the support!

Robert

1 Like

#36

Hi Robert,
here is the PR https://github.com/NeuBIAS/bise/pull/76
Now it needs to be deploy on production site. I’ll ring the bell!

1 Like

#37

Now working with biii.eu search… I PRed to @haesleinhuepf

It might be better to

  • indicate software type (component, collection, workflow)
  • limit search results to those tagged with “ImageJ” and “Fiji”?

1 Like

#38

Hi Kota,

good question:

Let the community decide.

If you search in Fijis search bar and have the BISE search activated, do you want to see results related to ImageJ/Fiji only, or do you want to see all search results from BISE?

  • only results from ImageJ/Fiji
  • all results

0 voters

You find an example search result searching for “Thresholding” here:
http://biii.eu/search?search_api_fulltext=Thresholding

Cheers,
Robert

0 Likes

#39

I voted “only from IJ/Fiji”, because for some search terms it becomes very long. If one needs to search regardless of the ecosystem, I think one should do search in biii.eu.

2 Likes

#40

I agree "only from IJ/Fiji”, if not crossed Search could be too many results. Then I will filter result in a new PR (not done yet )

1 Like