DOI: 10.5281/zenodo.10590347
title: Image datasets associated with Gut Analysis Toolbox

description: The images are sample image datasets associated with the software: Gut Analysis Toolbox (GAT).

The dataset contains immunofluorescence images of enteric neurons and glia labeled with different markers.  The data is mostly from mouse and human colon or small intestine. 

Channels corresponding to Hu labelling can be used for segmenting enteric neurons in GAT. 

Channels corresponding to GFAP (enteric glia) or neurons with markers labelling the cell body and processes (ChAT, Calbindin, Calretinin) can be used as a ganglia marker for segmenting the ganglia

The data is two-dimensional (2D) with some images having multiple channels. The data is mostly in tif format, except for one dataset that is czi (Fiji using bioformats or aicspylibczi in Python). Calcium imaging data is 2D+Time.

 

Data curated by: Pradeep Rajasekhar, Walter and Eliza Hall Institute of Medical Research, Australia

Data from INM lab, Monash University (mouse images)

Immunofluorescence images



 181107_ms_distal_colon_GFAP_Hu_40X.tif



Channel 1: GFAP

Channel 2: Hu








181107_ms_distal_colon_nNOS_GFAP_Hu_40X.tif (Same as above, but got an extra channel)









Channel 1: nNOS

Channel 2: GFAP

Channel 3: Hu




In both images above, GFAP can be used as ganglia segmentation channel in GAT using DeepImageJ.





ms_distal_colon_Hu_20X.tif











Hu









ms_distal_colon_Hu_40X_1.tif











Hu









Tilescan_GAT_ms_distal_colon_MP_hu.tif











Hu





Calcium imaging data (video)

• calcium_imaging_mouse_distal_colon_25X.tif

Tissue was incubated with calcium dye Fluo8-AM calcium dye (Myenteric wholemount from distal colon of mouse)

142 frames in total acquired at 1.162 frames per second. At frame 52, 100 uM of ATP is added which causes enteric glia, neurons and blood vessels to respond. This causes slow drifting in the field of view.

 

• mouse_GCamp_calcium_movement.tif

 

Wnt1-GCaMP3 mouse where GCamP3 is a genetically encoded calcium sensor expressed by enteric neurons and enteric glia

Imaging performed at Monash University. 745 frames in total acquired at 1.162 frames per second with drifting over time

Tissue source: Stamp & Hao laboratory, University of Melbourne.

 

Images from McQuade Lab, University of Melbourne



ms_28_wk_colon_DAPI_nNOS_Hu_10X.tif (mouse colon)

ms_28_wk_colon_DAPI_nNOS_Hu_10X.tif (mouse ileum)



Channel 1: DAPI

Channel 2: nNOS 

Channel 3: Hu








ms_distal_colon_nNOS_Hu_10X.czi    (This is a .czi file which can be opened in Fiji using bioformats or aicspylibczi in Python)









Channel 1: DAPI

Channel 2: nNOS 

Channel 3: Hu




Images from public repository (SPARC):



DYM_22_7_Pr_Chat_BYFP_DIN_GFP-g_nNOS-m_VIP-r_Hu-b.tif is a crop from File 100 05-07-2019 DYM 22 7 Pr Chat%3BYFP DIN GFP-g nNOS-m VIP-r Hu-b (Mouse Proximal Colon)

DYM_22_7_Pr_Hu_crop.tif is a crop from above.



Channel 1: Choline acetyltransferase

Channel 2: nNOS

Channel 3: Calretinin

Channel 4: Hu (pan-neuronal marker)




          Channel 1 and 3 can be used as ganglia segmentation channels in GAT using DeepImageJ.

 





146_02_14_20DYM8_6_mouse_Mid_Chat-g CalB-r CalR-b_max.tif is from File 146 02-14-20 DYM 8 6 Mid Chat-g CalB-r CalR-b (Mouse mid colon)



          No Hu staining, any channel could be used as ganglia segmentation channel in GAT using DeepImageJ.









Channel 1: ChAT

Channel 2: Calbindin

Channel 3: Calretinin





Reference:

Thanks goes to Marthe Howard for depositing the data in the SPARC repository.

Howard, M. (2021). 3D imaging of enteric neurons in mouse (Version 1) [Data set]. SPARC Consortium. https://doi.org/10.26275/9FFG-482D

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Multiplex data (Flinders University)

Multiplexing_H2202Desc_Layer 1_Ganglia1_Hu.zip is from:

Chen, B. N., Humenick, A., Yew, W. P., Peterson, R. A., Wiklendt, L., Dinning, P. G., Spencer, N. J., Wattchow, D. A., Costa, M., & Brookes, S. J. H. (2023). Types of Neurons in the Human Colonic Myenteric Plexus Identified by Multilayer Immunohistochemical Coding. Cellular and molecular gastroenterology and hepatology, 16(4), 573–605.

This data is a myenteric wholemount from the descending colon of a Human. It has 14 different markers, 6 different rounds of staining. Every round has pan-neuronal marker Hu as a reference marker.There are 19 images. The filenames follow the convention:

 

H2202Desc_layer num_ganglia num_markername.tif 

H2202 is the sample name, Desc means descending colon

Here layer num corresponds to the round of staining, so Layer3, means its the 3rd round of staining.

ganglia num is specified as multiple ganglia can be imaged from same tissue. 

markername corresponds to the marker used. 

 

Markers used are: Hu, 5HT, ChAT, NOS, CGRP, Enk, SP, Somat, VACht, NPY, Calbindin, Calretinin, NF, VIP

 

Abbreviations:

 



Hu: Pan-neuronal marker

5HT: Serotonin (5-Hydroxytryptamine)

ChAT: Choline acetyltransferase

nNOS: neuronal Nitric Oxide Synthase (NOS in these images are actually nNOS)

CGRP: Calcitonin Gene-Related Peptide

Enk: Enkephalin

SP: Substance P

Somat: Somatostatin

VACht: Vasoactive Intestinal Peptide (VIP) 

NPY: Neuropeptide Y

NF: neurofilament 200