TACI: An ImageJ Plugin for 3D Calcium Imaging Analysis

Summary

TrackMate Analysis of Calcium Imaging (TACI) is an open-source ImageJ plugin for 3D calcium imaging analysis that examines motion on the z-axis and identifies the maximum value of each z-stack to represent a cell's intensity at the corresponding time point. It can separate neurons overlapping in the lateral (x/y) direction but on different z-planes.

Abstract

Research in neuroscience has evolved to use complex imaging and computational tools to extract comprehensive information from data sets. Calcium imaging is a widely used technique that requires sophisticated software to obtain reliable results, but many laboratories struggle to adopt computational methods when updating protocols to meet modern standards. Difficulties arise due to a lack of programming knowledge and paywalls for software. In addition, cells of interest display movements in all directions during calcium imaging. Many approaches have been developed to correct the motion in the lateral (x/y) direction.

This paper describes a workflow using a new ImageJ plugin, TrackMate Analysis of Calcium Imaging (TACI), to examine motion on the z-axis in 3D calcium imaging. This software identifies the maximum fluorescence value from all the z-positions a neuron appears in and uses it to represent the neuron's intensity at the corresponding t-position. Therefore, this tool can separate neurons overlapping in the lateral (x/y) direction but appearing on distinct z-planes. As an ImageJ plugin, TACI is a user-friendly, open-source computational tool for 3D calcium imaging analysis. We validated this workflow using fly larval thermosensitive neurons that displayed movements in all directions during temperature fluctuation and a 3D calcium imaging dataset acquired from the fly brain.

Introduction

The level of intracellular calcium is a precise marker of neuronal excitability. Calcium imaging measures the changes in intracellular calcium to understand neuronal activity¹. Studies in neuroscience have increasingly used this method due to the development of techniques for measuring intracellular calcium concentration, including genetically encoded calcium indicators (GECIs), such as GCaMP^2,3, which can be noninvasively expressed in specific sets of neurons through genetic approaches. The lower costs of lasers and microscope components have also increased the use of calcium imaging

Protocol

1. Calcium imaging

1. Fly larvae preparation
   NOTE: Flies and larvae are maintained at 25 °C under a 12 h:12 h light:dark cycle.
   1. Anesthetize the flies with CO₂. Sort 20-45 males and 20-45 females into each fly vial, and give them at least 24 h to 48 h to recover from the CO₂ exposure.
      NOTE: Fly exposure to CO₂ should last for the shortest amount of time possible.
   2. To synchronize the larvae age, tap over the flies into new vials containing yeast granules, and allow them 4-8 h to lay eggs. Remove the flies by flipping them into new vials.
   3. Collect the larvae at 72 h usin....

Results

Workflow of 3D calcium imaging analysis
In this study, we developed a new ImageJ plugin, TACI, and described a workflow to track z-drift and analyze 3D calcium imaging that pinpoints the responses of individual cells appearing in multiple z-positions (Figure 1). This tool has four functions: RENAME, ORGANIZE, EXTRACT, and MERGE. First, if the image names are not compatible with the ORGANIZE

Discussion

This study developed a new ImageJ plugin, TACI, and described a workflow analyzing 3D calcium imaging. Many currently available tools focus on correcting the x/y motion, although motion on the z-axis also needs to be explicitly diagnosed or corrected⁶. During image acquisition in a live organism, movement on the z-axis is unavoidable even when the organism is immobilized, and some stimuli, such as temperature change, often cause significant z-drift. Increasing the height of the z-stacks will allow.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Blunt Fill Needel	BD	303129
Calcium chloride dihydrate	Fisher Scientific	10035-04-8	Fly food ingredient
Carbon dioxide	Airgas	UN1013	Size 200 High Pressure Steel Cylinder
CO2 bubbler kit	Genesee	59-180
Confocal microscope LSM880	Zeiss	4109002107876000	An inverted Axio Observer Z1, equipped with 5 lasers, 2 standard PMT detectors, 32-channel GaAsP dectectors, an Airyscan detector, and Definite Focus.2.
DAQami software	Measurement Computing
Dextrose	Genesee	62-113	Fly food ingredient
Drosophila Agar	Genesee	66-111	Fly food ingredient
Ethanol	Decon Labs, Inc.	64-17-5	Fly food ingredient
Fly line: Ir21a-Gal4	Dr. Paul Garrity lab		A kind gift
Fly line: Ir21a-Gal80	Dr. Lina Ni lab
Fly line: Ir68a-Gal4	Dr. Aravinthan DT Samuel lab		A kind gift
Fly line: Ir93a-Gal4	Dr. Paul Garrity lab		A kind gift
Fly line: UAS-GCaMP6	Bloomington Drosophila Stock Center	42750
Flypad	Genesee	59-114
General purpose forged brass regulator	Gentec	G152
Gibco PBS pH 7.4 (1x)	Thermo Fisher Scientific	10010-031
Green Drosophila tubing	Genesee	59-124
Heat transfer compound	MG Chemicals	860-60G
Heatsink	Digi-Key Electronics	ATS2193-ND	Resize to 12.9 x 5.5 cm
Illuminator	AmScope	LED-6W
Inactive Dry Yeast	Genesee	62-108	Fly food ingredient
Incubator	Pervical	DR-41VL	Light: dark cycle: 12h:12h; temperature: 25 °C; humidity: 40-50% RH.
Methyl-4-hydroxybenzoate	Thermo Scientific	126965000	Fly food ingrediete
Micro cover glass	VWR	48382-126	22 x 40 mm
Microscope slides	Fisher Scientific	12-544-2	25 x 75 x 1.0 mm
Nail polish	Kleancolor
Narrow Drosophila vials	Genesee	32-113RL
Objective	Zeiss	420852-9871-000	LD LCI Plan-Apochromat 25x/0.8 Imm Corr DIC M27
Peltier cooling module	TE Technology	TE-127-1.0-0.8	30 x 30 mm
Plugs	Genesee	49-102
Power Supply	Circuit Specialists	CSI1802X	10 volt DC 2.0 amp linear bench power supply
Princeton Artist Brush Nepture	Princeton Artist Brush Co.		Series 4750, size 2
Sodium potassium L-tartrate tetrahydrate	Thermo Scientific	033241-36	Fly food ingredient
Stage insert	Wienecke and Sinske	432339-9030-000
Stereo Microscope	Olympus	SZ61	Any stereo microscope works
T-Fitting	Genesee	59-123
Thermocouple data acquisition device	Measurement Computing	USB-2001-TC	Single channel
Thermocouple microprobe	Physitemp	IT-24P
Yellow Cornmeal	Genesee	62-101	Fly food ingredient
Z-axis piezo stage	Wienecke and Sinske	432339-9000-000